Biology subjects

St-Arnaud, M.

Publications and source records attributed to St-Arnaud, M..

5 recordsLinked to original sources

bioRxiv2023

Does soil history decline in influencing the structure of bacterial communities of Brassica napus host plants across different growth stages?

Soil history has been shown to condition future plant-soil microbial communities up to a year after being established. However, previous experiments have also illustrated that mature, adult plants can "re-write", or mask, different soil histories through host plant-soil microbial community feedbacks. This leaves a knowledge gap concerning how soil history influences bacterial community structure across different growth stages. Therefore, in this experiment we tested the hypothesis that previously established soil histories will decrease in influencing the structure of Brassica napus bacterial communities over the growing season. We used an on-going agricultural field experiment to establish three different soil histories, plots of monocrop canola (B. napus), or rotations of wheat-canola, or pea-barley-canola. During the following season, we repeatedly sampled the surrounding bulk soil, rhizosphere and roots of B. napus at different growth stages-- the initial seeding conditions, seedling, rosette, bolting, and flower-- from all three soil history plots. We compared the taxonomic composition and diversity of bacterial communities, as estimated using 16S rRNA metabarcoding, to identify any changes associated with soil history and growth stages on the different B. napus soil bacterial communities. We found that soil history remained significant across each growth stage in structuring the bulk soil and rhizosphere communities, but not the roots. This suggests that the host plants capacity to "re-write" different soil histories may be quite limited as key components that constitute the soil historys identity remain present and continue to impact bacterial communities. For agriculture, this highlights how previously established soil histories persist and may have important long-term consequences on future plant-microbe communities, including bacteria.

microbiology↗

bioRxiv2022

The effect of wheat genotype on its microbiome is more evident in roots than rhizosphere and is strongly influenced by time

Crop breeding has traditionally ignored the plant-associated microbial communities. Consideration of the interactions between plant genotype and associated microbiota is of value since different genotypes of the same crop often harbor distinct microbial communities which can influence the plant phenotype. However, recent studies have reported contrasting results, which led us to hypothesize that the effect of genotype is constrained by time (growth stage, year) and space (plant compartment). To test this hypothesis, we sampled bulk soil, rhizosphere soil and roots of 10 wheat genotypes, twice per year, for 4 years. DNA was extracted and regions of the bacterial 16S rRNA and CPN60 genes and the fungal ITS region were amplified and sequenced. The effect of genotype was highly contingent on the time of sampling and on the plant compartment sampled. Only for a few sampling dates, were the microbial communities significantly different across genotypes. The effect of genotype was most often significant for root microbial communities. The three marker genes used provided a highly coherent picture of the effect of genotype. Taken together, our results confirm that microbial communities in the plant environment strongly vary temporally and spatially and that this can mask the effect of genotype.

microbiology↗

bioRxiv2022

Metatranscriptomic response of the wheat holobiont to decreasing soil water content

Crops associate with microorganisms that help their resistance to biotic. However, it is not clear how the different partners of this association react during exposure to stresses. This knowledge is needed to target the right partners when trying to adapt crops to climate change. Here, we grew wheat in the field under rainout shelters that let through 100%, 75%, 50% and 25% of the precipitation. At the peak of the growing season, we sampled plant roots and rhizosphere, and extracted and sequenced their RNA. We compared the 100% and the 25% treatments using differential abundance analysis. In the roots, most of the differentially abundant (DA) transcripts belonged to the fungi, and most were more abundant in the 25% precipitation treatment. About 10% of the DA transcripts belonged to the plant and most were less abundant in the 25% precipitation treatment. In the rhizosphere, most of the DA transcripts belonged to the bacteria and were generally more abundant in the 25% precipitation treatment. Taken together, our results show that the transcriptomic response of the wheat holobiont to decreasing precipitation levels is more intense for the fungal and bacterial partners than for the plant.

microbiology↗

bioRxiv2022

Soil chemistry and soil history significantly structure oomycete communities in Brassicaceae crop rotations

Oomycetes are critically important soil microbial communities, especially for agriculture where they are responsible for major declines in yields. Unfortunately, oomycetes are vastly understudied compared to bacteria and fungi. As such, our understanding of how oomycete biodiversity and community structure varies through time in the soil remains poor. Soil history established by previous crops is one factor known to structure other soil microbes, but has not been investigated for its influence on oomycetes. In this study, we established three different soil histories in field trials; the following year these plots were planted with five different Brassicaceae crops. We hypothesized that the previously established soil histories would structure different oomycete communities, regardless of their current Brassicaceae crop host, in both the roots and rhizosphere. We used a nested-ITS amplicon strategy incorporated with MiSeq metabarcoding, where the sequencing data was used to infer amplicon sequence variants (ASVs) of the oomycetes present in each sample. This allowed us to determine the impact of different soil histories on the structure and biodiversity of the oomycete root and rhizosphere communities from the five different Brassicaceae crops. We found that each soil history structured distinct oomycete rhizosphere communities, regardless of different Brassicaceae crop hosts, while soil chemistry structured the oomycete communities more during a dry year. Interestingly, soil history appeared specific to oomycetes, but was less influential for bacterial communities previously identified from the same samples. These results advance our understanding of how different agricultural practices and inputs can alter edaphic factors to impact future oomycete communities. Examining how different soil histories endure and impact oomycete biodiversity will help clarify how these important communities may be assembled in agricultural soils. HighlightsO_LICrop rotations model how soil history impacts subsequent microbial communities C_LIO_LIBrassicaceae oilseed crops might mitigate pathogenic oomycetes C_LIO_LISoil history significantly structures oomycete communities C_LIO_LIOomycetes are significantly affected by soil chemistry C_LIO_LIBrassicaceae crop hosts weakly influence oomycete communities C_LI O_FIG O_LINKSMALLFIG WIDTH=115 HEIGHT=200 SRC="FIGDIR/small/499733v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1f2160aorg.highwire.dtl.DTLVardef@84fbeforg.highwire.dtl.DTLVardef@b81689org.highwire.dtl.DTLVardef@1cfacf4_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

What's past is past, mostly: Brassicaceae host plants mask the feedback from the previous year's soil history on bacterial communities, except when the Brassicaceae hosts experience drought

Previous soil history and the current plant hosts are two plant-soil feedbacks that operate at different time-scales to influence the structure soil bacterial communities. In this study, we used a MiSeq metabarcoding strategy to describe the impact of five Brassicaceae host plant species, and three different soil histories, on the structure of their bacterial root and rhizosphere communities at full flower. We found that the Brassicaceae host plants were consistently significant in structuring the bacterial communities. Four host plants (Sinapis alba, Brassica napus, B. juncea, B. carinata) formed nearly the same bacterial communities, regardless of soil history. Camelina sativa host plants structured phylogenetically distinct bacterial communities compared to the other hosts, particularly in their roots. Soil history established the previous year was only a significant factor for bacterial community structure when the feedback of the Brassicaceae host plants was weakened, potentially due to limited soil moisture during a dry year. Understanding how plant-soil feedbacks operate at different time-scales and are involved in how microbial communities are structured is a pre-requisite for employing microbiome technologies in improving agricultural systems.

plant biology↗