Soil protists are an important part of the microbial community in the rhizosphere. Plants grown with protists fare better than plants grown without protists.

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.

Protists play important roles in shaping the microbial community of the rhizosphere. However, there is still a limited understanding of how plants shape the protist community, and how well protist isolate collections might represent rhizosphere protist composition and function in downstream studies. We sought to determine whether maize roots select for a distinct protist community in the field, and whether the common or dominant members of that community are readily culturable using standard protist isolation methods. We sequenced 18S and 16S rRNA genes from the rhizospheres of maize grown in two sites, and isolated 103 protists into culture from the same roots. While field site had the greatest effect, rhizospheres in both sites had distinct protist composition from the bulk soils, and certain taxa were enriched in both sites. Enriched taxa were correlated to bacterial abundance patterns. The isolated protists represented six supergroups, and the majority corresponded to taxa found in the sequencing survey. Twenty-six isolates matched eight of the 89 core rhizosphere taxa. This study demonstrates that maize roots select for a distinct protist community, but also illustrate the potential challenges in understanding the function of the dominant protist groups in the rhizosphere.

The rhizosphere is the region of soil directly influenced by plant roots. The microbial community in the rhizosphere includes fungi, protists, and bacteria, all of which play a significant role in plant health. The beneficial bacterium Sinorhizobium meliloti infects growing root hairs on nitrogen starved leguminous plants. Infection leads to the formation of a root nodule, where S. meliloti converts atmospheric nitrogen to ammonia, the usable form of nitrogen for plants. However, S. meliloti, often found in biofilms, travels slowly; whereas infectible root hairs are found at the growing root tip, potentially causing many root hairs to remain uninfected by S. meliloti when it is delivered as a seed inoculant. Soil protists are an important component of the rhizosphere system who prey on soil bacteria and have been known to egest undigested phagosomes. We show that the soil protist, Colpoda sp., plays an important role in transporting S. meliloti down Medicago truncatula roots. By using pseudo-3D soil microcosms we directly observed the presence of fluorescently labelled S. meliloti along M. truncatula roots and track the displacement of bacteria over time. In the presence of Colpoda sp., S. meliloti was detected 44 mm, on average, farther down the roots, compared with the Bacteria Only Treatment. Facilitating bacterial transport may be an important mechanism whereby soil protists promote plant health. Protist facilitated transport as a sustainable agriculture biotechnology has the potential to boost efficacy of bacterial inoculants, avoid overuse of nitrogen fertilizers, and enhance performance of no-till farming practices.