Context dependent fungal and bacterial soil community shifts in response to recent wildfires in the Southern Appalachian Mountains

Grillo

Podowski

et al. 2020

Preprint

Self Cite

Background Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities. Results Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment × soil origin and compartment × plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless all compartments were dominated by Ensifer , the genus of rhizobia that forms root nodule symbiosis with M. truncatula , and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere. Conclusions Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis towards a more mechanistic understanding of plant microbiomes.

Section: Methodsmentioning

confidence: 99%

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

Grillo

Podowski

et al. 2020

Preprint

Self Cite

“…The V4 region of the rRNA gene repeat was amplified in a two-step process using the forward primer nexF-N[3-6]-515f and the reverse primer nexR-N[3-6]-806r. [54][55][56] These forward and reverse primer constructs include the following: bacterial primers (515f and 806r), Nextera forward (nexF) and reverse (nexR) sequencing primers, and four identical primers comprised of ambiguous nucleotides mixed to equal molarity (N [3][4][5][6]) to increase sequence variation. Secondary PCRs were conducted in 25 μL reactions using 12.5 μL PCR Master Mix (as above), 2.5 μL of primary PCR product that was used as template DNA, 7.5 μL molecular grade water, and 2.5 μL barcoded secondary primers.…”

Section: Dna Extractions and Library Preparationmentioning

confidence: 99%

“…55 PCR parameters were 98°C for 30 s, 8 cycles of 98°C for 20 s, 50°C for 30 s, 72°C for 40 s, and final extension at 72°C for 10 min. 56 The final amplicon constructs produced after 32 cycles were P5…”

Section: Dna Extractions and Library Preparationmentioning

confidence: 99%

A novel role for the pineal gland: Regulating seasonal shifts in the gut microbiota of Siberian hamsters

Shor

Journal of Pineal Research

Freeman

2020

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The gut microbiota plays a significant role in a variety of host behavioral and physiological processes. The mechanisms by which the gut microbiota and the host communicate are not fully resolved but include both humoral and direct neural signals. The composition of the microbiota is affected by internal (host) factors and external (environmental) factors. One such signal is photoperiod, which is represented endogenously by nocturnal pineal melatonin (MEL) secretion. Removal of the MEL signal via pinealectomy abolishes many seasonal responses to photoperiod. In Siberian hamsters (Phodopus sungorus), MEL drives robust seasonal shifts in physiology and behavior, such as immunity, stress, body mass, and aggression. While the profile of the gut microbiota also changes by season, it is unclear whether these changes are driven by pineal signals. We hypothesized that the pineal gland mediates seasonal alterations in the composition of the gut microbiota. To test this, we placed pinealectomized and intact hamsters into long or short photoperiods for 8 weeks, collected weekly fecal samples, and measured weekly food intake, testis volume, and body mass. We determined microbiota composition using 16S rRNA sequencing (Illumina MiSeq). We found significant effects of treatment and time on the abundances of numerous bacterial genera. We also found significant associations between individual OTU abundances and body mass, testis mass, and food intake, respectively. Finally, results indicate a relationship between overall community structure, and body and testis masses. These results firmly establish a role for the pineal gland in mediating seasonal alterations in the gut microbiota. Further, these results identify a novel neuroendocrine pathway by which a host regulates seasonal shifts in gut community composition, and indicates a relationship between seasonal changes in the gut microbiota and seasonal physiological adjustments.

“…Briefly loading scores from each of the first 10 NMDS axes (representing over >99% variation) were used as dependent variables in random effects models using restricted maximum likelihood (REML) to determine the percentage of variation explained by each treatment, interactions, and residuals. These variance partitions were then weighted by the percentage of community variation explained by the NMDS axis (R 2 ) (see [120]) then scaled and summed across all tested axes to total 100%.…”

Section: Diversity Communities and Statisticalmentioning

confidence: 99%

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

Grillo

Podowski

et al. 2020

Preprint

Self Cite

Background: Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities.Results: Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment x soil origin and compartment x plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless all compartments were dominated by Ensifer, the genus of rhizobia that forms root nodule symbiosis with M. truncatula , and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere.Conclusions: Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis towards a more mechanistic understanding of plant microbiomes.