Biology subjects

Taerum, S. J.

Publications and source records attributed to Taerum, S. J..

6 recordsLinked to original sources

bioRxiv2026

A qPCR method facilitates study of absolute abundance, ecology, and inoculation fate of ciliate predators on the leaf surface

Predatory protists are important in shaping terrestrial microbial ecosystems, but their roles in the phyllosphere, or the communities on aerial plant surfaces, are poorly understood. Previous work found that the order Colpodida dominated heterotrophic protist communities in the phyllosphere. While most protists were sporadically present, a few Colpodida variants were prevalent and abundant, indicating that these variants may represent species adapted to the phyllosphere. To identify these organisms, we cultured colpodids from field-collected tomato leaves and performed phylogenetic analysis of the 18S rRNA gene. Five of nine independent isolates matched the most prevalent Colpodida variant previously identified as leaf-enriched through amplicon sequencing, and these isolates comprised a novel clade of Paracolpoda steinii. When compared to a maize root isolate of Colpoda inflata, an abundant rhizosphere ciliate, a P. steinii isolate was similar in size and growth yield on E. coli, but grew to higher yields and formed large cyst clusters when incubated with model phyllosphere bacteria prey Erwinia and Pseudomonas. We developed and validated quantitative PCR (qPCR) methods for detection and cell abundance estimation of the P. steinii phyllosphere clade, C. inflata, and the order Colpodida in environmental samples. In inoculated greenhouse plants, qPCR-estimated protist populations matched measured inoculum levels, and protist inoculum was still detectable after five days. In an uninoculated tomato field, P. steinii was detected on all plants, with greatest abundances observed in lower leaves and after a rain event. P. steinii comprised up to 18.7% of total leaf Colpodida populations, which were estimated at up to [~]1400 organisms per gram of fresh weight. The findings demonstrate that Colpodida communities are consistently present on tomato leaves, dynamically affected by the abiotic environment, and include significant populations of P. steinii. We propose that the P. steinii isolates and qPCR tools presented can be used as a model system to investigate colonization and distribution patterns, biotic interactions, genetic adaptations, and agricultural applications of leaf predation.

microbiology↗

bioRxiv2025

Rhizosphere-colonizing bacteria persist in the protist microbiome

Soils contain diverse predatory protists that affect the abundance and behavior of rhizosphere bacteria, including bacteria that may benefit plant health. Protists also harbor their own bacterial microbiomes, including transient and extracellular associates, but it is not known whether the protist microbiome affects the plant rhizosphere. To address this question, we profiled the bacterial microbiomes of eight evolutionarily diverse rhizosphere protist isolates after two years of continuous laboratory culture. We then compared the protist culture microbiomes to maize rhizosphere communities six weeks after protist inoculation. Introduction of protists enriched 13 protist-associated bacterial amplicon sequence variants (ASVs) in the rhizosphere, which comprised [~]10% of the rhizosphere bacterial community. Additional bacterial ASVs ranked highly in abundance in both rhizosphere and protist microbiomes; together, a median 47% of the protist microbiome was enriched or abundant in the rhizosphere. Inoculation with some of the protist cultures positively affected root biomass traits, but a protist mixture had no effect, indicating that the impact of protist holobionts on plant growth is context-dependent. Isolates of protist-associated bacteria had both positive and negative effects on protist growth in culture, suggesting that the bacteria use multiple strategies to survive in proximity to predators. This study demonstrates that even after prolonged laboratory culture, evolutionarily diverse rhizosphere protists host bacterial microbiomes dominated by plant-colonizing bacteria that impact the rhizosphere microbiome after inoculation. The findings suggest that protists may contribute to the rhizosphere as part of the soil microbial seedbank, and identify bacterial groups that may be important to the plant-protist interaction. ImportanceUnderstanding the impact of predatory protists on the plant microbiome will be essential to deploy protists in sustainable agriculture. This study shows that eight rhizosphere protist isolates hosted diverse and distinct bacterial communities, and that a large proportion of these bacteria could be found colonizing the maize root environment long after protists were introduced. This study demonstrates that maize rhizosphere bacteria can persist for years in the protist microbiome, indicating that extremely diverse eukaryotes could help select and maintain rhizosphere bacteria in the absence of the plant.

microbiology↗

bioRxiv2024

Transcriptome and evolutionary analysis of Pseudotrichomonas keilini, a free-living anaerobic eukaryote

The early evolution of eukaryotes and their adaptations to low-oxygen environments are fascinating open questions in biology. Genome-scale data from novel eukaryotes, and particularly from free-living lineages, are key to answering these questions. The Parabasalia are an ancient lineage of anaerobes, and the most speciose lineage of Metamonada, a major lineage of eukaryotes. The most well-studied metamonads are parasitic parabasalids including Trichomonas vaginalis, Tritrichomonas foetus, and Giardia intestinalis, but very little genome-scale data is available for free-living members of the group. Here, we sequenced the transcriptome of Pseudotrichomonas keilini, a free-living parabasalian. Comparative genomic analysis indicated that P. keilini possesses a metabolism and gene complement that are in many respects similar to its parasitic relative Trichomonas vaginalis, and that in the time since their most recent common ancestor, it is the Trichomonas vaginalis lineage that has experienced more genomic change, likely due to the transition to a parasitic lifestyle. Features shared between P. keilini and Trichomonas vaginalis include a hydrogenosome (anaerobic mitochondrial homologue) that we predict to function much as in Trichomonas vaginalis, and a complete glycolytic pathway that is likely to represent one of the primary means by which P. keilini obtains ATP. Phylogenomic analysis indicates that P. keilini branches within a clade of endobiotic parabasalids, consistent with the hypothesis that different parabasalid lineages evolved towards parasitic or free-living lifestyles from an endobiotic, anaerobic or microaerophilic common ancestor.

evolutionary biology↗

bioRxiv2021

A dual sequence and culture-based survey of maize rhizosphere protists reveals dominant,plant-enriched, and culturable community members

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. Originality-Significance StatementThis is the first study comparing cultivation-dependent and independent methods for studying the protist community of plant roots, and the first untargeted analysis of the maize rhizospheres effect on protist communities. We show that maize in different sites select for distinct communities and overlapping enriched taxa, but that isolating the most important plant-associated protists may be a challenge for researchers.

microbiology↗

bioRxiv2021

Whats under the Christmas tree? Soil acidification alters fir tree rhizosphere bacterial and eukaryotic communities, their interactions, and functional traits

pH has been identified as a master regulator of the soil environment, controlling the solubility and availability of nutrients. As such, soil pH exerts a strong influence on indigenous microbial communities. In this study we describe a soil acidification experiment and the resulting effects on the rhizosphere communities of fir trees on a Christmas tree plantation. The acidification treatment reduced the pH of bulk soil by [~]1.4 pH units and was associated with reduced Ca, Mg, and organic matter content. Similarly, root chemistry differed due to soil acidification with roots in acidified soils showing significantly higher Al, Mn, and Zn content and reduced levels of B and Ca. 16S rRNA and 18S rRNA gene sequencing was pursued to characterize the bacterial/archaeal and eukaryotic communities in the rhizosphere soils. The acidification treatment induced dramatic and significant changes in the microbial populations, with thousands of 16S RNA gene sequence variants and hundreds of 18S rRNA gene variants being significantly different in relative abundance between the treatments. Additionally, co-occurrence networks showed that bacterial and eukaryotic interactions, network topology, and hub taxa were significantly different when constructed from the control and acidified soil rRNA gene amplicon libraries. Finally, metagenome sequencing showed that the taxonomic shifts in the community resulted in alterations to the functional traits of the dominant community members. Several biochemical pathways related to sulfur and nitrogen cycling distinguished the metagenomes generated from the control and acidified soils, demonstrating the myriad of effects soils acidification induces to rhizosphere microbes. IMPORTANCESoil pH has been identified as the property that exerts the largest influence on soil microbial populations. We employed a soil acidification experiment to investigate the effect of lowering soil pH on the bacterial and eukaryotic populations in the rhizosphere of Christmas trees. Acidification of the soils drove alterations of fir tree root chemistry and large shifts in the taxonomic and functional composition of the communities, involving pathways in sulfur and nitrogen cycling. These data demonstrate that soil pH influences are manifest across all organisms inhabiting the soil, from the host plant to the microorganisms inhabiting the rhizosphere soils. Thus, pH is an important factor that needs to be considered when investigating soil and plant health, the status of the soil microbiome, and terrestrial nutrient cycling.

microbiology↗

bioRxiv2020

Validation of a PNA clamping method for reducing host DNA amplification and increasing eukaryotic diversity in rhizosphere microbiome studies

Protists and microscopic animals are important but poorly understood determinants of plant health. Plant-associated eukaryotes could be surveyed by high-throughput sequencing of 18S ribosomal RNA (rRNA) genes, but the abundance of plant DNA in rhizosphere samples makes 18S rRNA gene amplification with universal primers unfeasible. Here we applied a pipeline to generate peptide nucleic acid (PNA) clamps to suppress the amplification of plant host DNA during 18S rRNA gene library preparation. We designed a PNA clamp, PoacV9_01, specific to the V9 region of the 18S rRNA gene for plants in the family Poaceae. PoacV9_01 suppressed the amplification of five species of grain crops in quantitative PCR reactions. In an 18S rRNA gene sequencing survey of the rhizosphere of maize, PoacV9_01 reduced the relative abundance of plant reads from 65% to 0.6%, while drastically increasing the number and diversity of animal, fungal, and protist reads detected. Thus, PoacV9_01 can be used to facilitate the study of eukaryotes present in grass phytobiomes. In addition, the pipeline developed here can be used to develop PNA clamps that target other plant species.

microbiology↗