Holobiont bacterial community assembly processes are an essential element to understanding the plant microbiome. To elucidate these processes, leaf, root, and rhizosphere samples were collected from ...eight lines of Brassica napus in Saskatchewan over the course of 10 weeks. We then used ecological null modeling to disentangle the community assembly processes over the growing season in each plant part. The root was primarily dominated by stochastic community assembly processes, which is inconsistent with previous studies that suggest of a highly selective root environment. Leaf assembly processes were primarily stochastic as well. In contrast, the rhizosphere was a highly selective environment. The dominant rhizosphere selection process leads to more similar communities. Assembly processes in all plant compartments were dependent on plant growth stage with little line effect on community assembly. The foundations of assembly in the leaf were due to the harsh environment, leading to dominance of stochastic effects, whereas the stochastic effects in the root interior likely arise due to competitive exclusion or priority effects. Engineering canola microbiomes should occur during periods of strong selection assuming strong selection could promote beneficial bacteria. For example, engineering the microbiome to resist pathogens, which are typically aerially born, should focus on the flowering period, whereas microbiomes to enhance yield should likely be engineered postflowering as the rhizosphere is undergoing strong selection.
In order to harness the microbiome for more sustainable crop production, we must first have a better understanding of microbial community assembly processes that occurring during plant development. This study examines the bacterial community assembly processes of the leaf, root, and rhizosphere of eight different lines of Brassica napus over the growing season. The influence of growth stage and B. napus line were examined in conjunction with the assembly processes. Understanding what influences the assembly processes of crops might allow for more targeted breeding efforts by working with the plant to manipulate the microbiome when it is undergoing the strongest selection pressure.
Land-use change and climatic variability are significant drivers for the loss of ecosystem services and soil quality in the prairie pothole region (PPR) wetland systems. Land-use induced changes in ...groundwater table and salinity may influence biogeochemical processes facilitated by extracellular enzymes (EEs) involved in soil organic matter (SOM) decomposition. The effects of changing groundwater table and salinity on β-glucosidase (BG), N-acetyl glucosaminidase (NAG), and alkaline phosphatase (AP) activities were assessed in wetland soils collected from three different adjacent riparian land-use practices in the PPR. In a microcosm study conducted over ten weeks, soils were treated with groundwater salinity (control, 6 mS cm
−1
, and 12 mS cm
−1
) and declining groundwater table depths. Extracellular enzyme activities (EEAs) differed significantly (
p
< 0.05) among soils from different land-uses and between groundwater table depths. The impact of groundwater salinity on soil EEAs were non-significant (
p
> 0.05). Soil EEAs were significantly higher in soils from pasture, suggesting that the land-use effects resulted from background SOC and TN. Soil EEAs significantly (
p
< 0.05) reduced under a deeper groundwater table depth, except reverse for BG in site B, indicated that the lowered groundwater table could lead to transitory drought stress for SOM decomposers.
Graphical Abstract
Diverse crop rotations can improve crop productivity but impacts on the interaction of soil nutrient cycling and the soil and root-associated microbiomes are not well understood. Here, we analysed ...16S rRNA and ITS DNA amplicons of soil, rhizosphere and roots from two Canadian long-term field experiments, wheat grown in Saskatchewan and corn grown Ontario. Together with soil biogeochemical analysis, we determined that long-term diverse rotations and cereal monocropping affected the composition of soil organic matter, nutrient cycling and selected bacterial and fungal microbiomes. Differential abundance analysis identified 27 bacterial amplicon sequence variants that were more abundant in the soil and rhizosphere of monocropped corn that were classified as Ktedonobacteria and Actinomycetales. Both wheat and corn samples showed significant variation in the abundance of several saprophytic Sordariomycetes. Monocropping increased lignin by 56% in corn and 25% in wheat, demonstrating shifts in soil organic matter composition in the two systems, although no differences in amino sugars were observed. Depending on sample type, soil total lignin and phosphatase enzyme activity were correlated (p < 0.05) with variation in bacterial and fungal community composition along with available N in corn and β-glucosidase in wheat. Our results indicate that over the long-term, reduced cropping diversity altered soil nutrient cycling and soil, rhizosphere and root microbiomes corresponding with reduced yields in the monocropped corn and wheat systems.
•Long-term diverse rotations affected SOM composition in corn and wheat systems.•Microbiomes differences were larger in soil vs. rhizosphere and root.•Changes in microbiome composition were correlated to differences in SOM.•Monocropping altered C and N cycling correlating with some microbiome differences.
The plant root microbiome can enhance yield in crops, but whether this effect is due to one yield-promoting bacterial community consisting of key taxa, or multiple configurations of taxa with ...different traits is unclear. A changing climate and the need to reduce carbon-intensive agricultural inputs has spurred breeding programs to explore holobiont approaches to optimizing crop yields. Here we used an extensive dataset of >1300 Brassica napus (a key oilseed crop) root samples across 4 trials and 16 varieties in a novel, robust analytical pipeline to decipher the beneficial root-associated bacterial communities associated with B. napus yield performance. We found three taxonomically distinct, but phylogenetically similar communities associated with leaf development, anthesis, and seed development that were linked to crop yield performance across multiple years and sites. Here we show B. napus is associated with not one, but several phenology-dependent yield-promoting root bacterial communities that influence seed yield via different, and yet undetermined, mechanisms. Therefore, we need to consider the relationship between B. napus phenology, and holobiont community assembly and function in selecting microbiome associated traits for use in breeding programs.
•Crop yield-enhancing root microbiomes contain not one, but multiple groups of key taxa.•Three taxonomically distinct, but phylogenetically similar microbiomes increase B. napus yield.•Yield-promoting bacteria were associated with B. napus phenology across multiple years and sites.
The soil microbial community regulates decomposition of plant litter, but little is known about how the composition of the community responds to litter quality. To evaluate this, we applied ...13C-labelled oat Avena sativa leaf or stem litter to soil at a rate of 5 mg C g−1 soil and incubated it at 20 °C for 170 days. We measured total C mineralized and litter-derived C remaining in soil over the incubation. Quantitative real-time PCR and Illumina MiSeq sequencing of marker genes were used to characterize shifts in abundance and composition of bacteria and fungi. We found no difference in litter-derived C remaining in the amended soils during the incubation; but more C (~23%) was mineralized from soil amended with leaf litter than those amended with stems, suggesting that leaf litter enhanced decomposition of the native soil organic matter. Leaf and stem litter supported the growth of bacteria and fungi throughout the incubation, but fungal growth and the fungal to bacterial ratio were more pronounced with the addition of stem litter. These changes in relative abundance as well as more pronounced shifts in fungal community structure in stem vs. leaf litter amended soils highlights the importance of fungi in degrading relatively resistant fractions of the lignin-enriched stem litter. Unlike the control soil (no litter added), the modularity (i.e., communities with some degree of independence) of co-occurrence in microbial networks increased, and this coincided litter-induced enrichment of specific taxa and with reduced alpha diversity. Leaf addition enriched a few bacterial (e.g., Bacilli) and many fungal (e.g., Nectriaceae, Didymellaceae, and Stachybotryaceae) taxa, whereas stem addition caused enrichment of fungi (e.g., Trichocomaceae and Chaetomiaceae) that are known to degrade resistant plant material. The findings of this study show that litter composition has a stronger influence on the composition of fungal than bacterial communities. Our results also suggest that some key fungal taxa have greater advantage in degrading relatively resistant plant material thereby supporting the growth of other bacterial and fungal taxa through release of simple, more degradable, compounds.
•More C (~23%) was mineralized from soil amended with leaf than stem litter.•Recovery of litter-derived C from leaf- and stem-amended soils did not differ.•High quality litters may enhance decomposition of the native soil organic matter.•Fungi showed stronger response than bacteria to litters of different quality.•Stem addition enriched cellulolytic fungi such as Trichocomaceae and Chaetomiaceae.
Soil temperature affects the rate of C-cycle processes by influencing the activities of microbial communities but little is known about whether the effects on these communities are consistent in ...different soils. We studied bacterial and fungal communities in six different soils, originating from two different Canadian climatic regions and incubated for three years at a common field site under ambient or warming (ca. +4.6 °C for 653 d of warming) conditions. Similar to early responses (reported after 295 d of warming), soil respiration is consistently higher (up to 2.8-fold) for 653 d of warming. However, soil origin-related differences in the community structure of bacteria were smaller at the end of the experiment, suggesting that environmental factors and management practices are important in shaping the structure of communities, but that this is a cumulative effect over time. In contrast, warming-induced shifts were greater and consistent across soils after longer period of soil warming. These shifts coincided with significant increases in the relative proportions of some potentially copiotrophic bacteria (e.g., Thermoleophilia, Alphaproteobacteria, and Bacilli). Fungal responses to warming, determined at the end of incubation, were largely soil-specific. The relative proportions of some fungi (e.g., Nectriaceae) increased with warming while several other taxa (e.g., Mortierellaceae and Lasiosphaeriaceae) showed significant reductions with warming. Unlike community structure, differences in the DNA content, microbial biomass carbon (MBC), and abundance of bacteria or fungi between the control and warmed soils were minor. This might be related to depletion of readily available substrates because measurements were made a year after the annual addition of litter. Our observation that community shifts became more pronounced over time suggests that these differences may have been realized through physiological temperature optima and through resulting shifts in resource availability.
•Responses of microbial communities to warming were studied in diverse soils.•Soils were artificially warmed (ca. +4.6 °C) for 653 days in the field.•Soil respiration was consistently higher in the warmed soils.•Warming-induced shifts in community structure were consistent across soils.•Some potentially copiotrophic bacteria and fungi were enriched in the warmed soils.
The plant microbiome is a key driver of plant health and agroecosystem functioning. This study used internal transcribed spacer (ITS) amplicon sequencing to examine the dynamics of root-associated ...fungal microbiomes in genetically-diverse Brassica napus genotypes following highly resolved sampling across growth stages at multiple sites in Saskatchewan, Canada. Across all samples including individual B. napus genotypes, sampling times and sites (n = 936 for both roots and rhizosphere), genotype was associated with only 2% of variance in fungal community structure, which was mostly driven by site-year (67% of variance for root and 79% for rhizosphere). Within a single site, this influence increased to between 4 and 16% of root and 5–13% of rhizosphere community variance, indicating genotype-specific adaptation to site conditions across the growing season. A single amplicon sequence variant (ASV) of Olpidium brassicae accounted for over 88% of the root fungal ASVs at two of the three sites. Despite O. brassicae dominance, a diverse fungal core microbiome consisting of 38 ASVs was detected in all genotypes of each site-year. We also identified 13 ASVs that were highly associated with B. napus yield; common between the rhizosphere and root, Gibberella baccata was negatively correlated with yield while Nectria ramulariae and a Tetracladium sp. were positively correlated with yield. The presence of a diverse core microbiome, dominated by O. brassicae, and identification of taxa associated with B. napus yield performance across a variety of environments reveal strategic targets for better understanding the role of the root microbiome in B. napus production.
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