Soil moisture is a strong determinant of microbial activity exerting dominant control over gaseous and liquid diffusion rates and affecting O2 and substrate availability. Often, measures of microbial ...community structure and soil moisture status fail to inform our understanding of soil processes, particularly those that are governed by complex feedbacks between substrate availability and environmental conditions (e.g. nitrogen transformations). Nitrous oxide (N2O) emissions, although conceptually regulated by soil moisture, are notoriously difficult to predict based on soil water content and nutrient status. Here, we studied agricultural soils under wetting, drying, and static moisture conditions to assess the impact of current and previous moisture on bacterial 16S rRNA composition; transcription of amoA, hao, norB, and nosZ; and net N2O production. Microbial community composition was dependent on previous moisture. As soils dried, bacterial rRNA contained fewer and more evenly distributed genera. We hypothesize that this was linked to the evenness of resource distribution as controlled by differences in substrate diffusion in wetting vs. drying conditions. N2O flux depended on previous, as well as current, soil moisture status and this legacy effect was greatest at 80% water filled pore space. Overall, we found that previous moisture affected microbial activity, transcription, composition and ultimately, N2O emissions. Our study demonstrates that, for soil microorganisms and processes, it is not only what soil moisture is, but also what it was that is important.
•Nitrous oxide flux depended on previous, as well as current, soil moisture.•Wetting and drying strongly affected nitrifier and denitrifier transcript abundance.•Direction of soil moisture change altered bacterial community characteristics.•The effect of soil moisture was greatest at 80% WFPS.
Aim
Incorporating non-bloat legumes into grass pastures can reduce enteric methane and alter cattle urinary urea N output by increasing protein intake. Deposition of high urea N urine influences ...soil N-cycling microbes and potentially N
2
O production. We studied how urine urea N concentration affects soil nitrifier and denitrifier abundances, activities, and N
2
O production.
Methods
15
N
13
C-labelled urea dissolved in cattle urine was added at 3.5 and 7.0 g L
−1
to soils from a grazed, non-bloat legume pasture and incubated under controlled conditions. CO
2
, N
2
O,
13
C-CO
2
, and
15
N-N
2
O production were quantified over 240 h, along with nitrifier and denitrifier N-cycling genes and mRNA transcripts.
Results
High urea urine increased total N
2
O relative to the control; low urea was not significantly different from the control or the high urea treatment. As a result, N
2
O-N emission factors were not significantly different between the low urea treatment (1.17%) and high urea treatment (0.94%). Doubling urea concentration doubled CO
2
-C
urea
and N
2
O-N
urea
but not total N
2
O-N. Urine addition initially inhibited then increased AOB transcripts and gene abundances.
nirK
and
nirS
transcript abundances indicated that denitrification by ammonia oxidizers and/or heterotrophic denitrifiers dominated N
2
O production. Urine addition increased
nosZ-II
vs.
nosZ-I
transcripts, improving soil N
2
O reduction potential.
Conclusion
Characterizing this interplay between nitrifiers and denitrifiers improves the understanding of urine patch N
2
O sinks and source dynamics. This mechanistic information helps to explain the constrained short-term N
2
O emissions observed in response to excess urine N excretion from cattle consuming high protein diets, e.g. non-bloat legumes.
Aims
Phyllosphere bacteria play critical roles in plant growth promotion, disease suppression and global nutrient cycling but remain understudied.
Methods
In this project, we examined the bacterial ...community on the phyllosphere of eight diverse lines of
Brassica napus
for ten weeks in Saskatoon, Saskatchewan Canada.
Results
The bacterial community was shaped largely by plant growth stage with distinct communities present before and after flowering. Bacterial diversity before flowering had 111 core members with high functional potential, with the peak of diversity being reached during flowering. After flowering, bacterial diversity dropped quickly and sharply to 16 members of the core community, suggesting that the plant did not support the same functional potential anymore.
B. napus
line had little effect on the larger community, but appeared to have more of an effect on the rare bacteria.
Conclusions
Our work suggests that the dominant bacterial community is driven by plant growth stage, whereas differences in plant line seemed to affect rare bacteria. The role of these rare bacteria in plant health remains unresolved.
The development of microbial networks is central to ecosystem functioning and is the hallmark of complex natural systems. Characterizing network development over time and across environmental ...gradients is hindered by the millions of potential interactions among community members, limiting interpretations of network evolution. We developed a feature selection approach using data winnowing that identifies the most ecologically influential microorganisms within a network undergoing change. Using a combination of graph theory, leave-one-out analysis, and statistical inference, complex microbial communities are winnowed to identify the core organisms responding to external gradients or functionality, and then network development is evaluated against these externalities. In a plant invasion case study, the winnowed microbial network became more influential as the plant invasion progressed as a result of direct plant-microbe links rather than the expected indirect plant-soil-microbe links. This represents the first use of structural equation modeling to predict microbial network evolution, which requires identification of keystone taxa and quantification of the ecological processes underpinning community structure and function patterns.
Seeds are reproductive structures able to carry and transfer microorganisms that play an important role in plant fitness. Genetic and external factors are reported to be partly responsible for the ...plant microbiome assemblage, but their contribution in seeds is poorly understood. In this study, wheat, canola, and lentil seeds were analyzed to characterize diversity, structure, and persistence of seed-associated microbial communities. Five lines and 2 generations of each crop were subjected to high-throughput amplicon sequencing of the 16S rRNA and internal transcribed spacer (ITS) regions. Bacterial and fungal communities differed most by crop type (30% and 47% of the variance), while generation explained an additional 10% and 15% of the variance. The offspring (i.e., generation harvested in 2016 at the same location) exhibited a higher number of common amplicon sequence variants (ASVs) and less variability in microbial composition. Additionally, in every sample analyzed, a “core microbiome” was detected consisting of 5 bacterial and 12 fungal ASVs. Our results suggest that crop, genotype, and field environmental conditions contributed to the seed-associated microbial assemblage. These findings not only expand our understanding of the factors influencing the seed microbiome but may also help us to manipulate and exploit the microbiota naturally carried by seeds.
Long-term contrasts in agricultural management can shift soil resource availability with potential consequences to microbial carbon (C) use efficiency (CUE) and the fate of C in soils. Isothermal ...calorimetry was combined with
C-labeled glucose stable isotope probing (SIP) of 16S rRNA genes to test the hypothesis that organically managed soils would support microbial communities with greater thermodynamic efficiency compared to conventional soils due to a legacy of lower resource availability and a resultant shift toward communities supportive of more oligotrophic taxa. Resource availability was greater in conventionally managed soils, with 3.5 times higher available phosphorus, 5% more nitrate, and 36% more dissolved organic C. The two management systems harbored distinct glucose-utilizing populations of
and
, with a higher
:
ratio (2.4 vs. 0.7) in conventional soils. Organically managed soils also harbored notable activity of
. Thermodynamic efficiency indices were similar between soils, indicating that glucose was metabolized at similar energetic cost. However, differentially abundant glucose utilizers in organically managed soils were positively correlated with soil organic matter (SOM) priming and negatively correlated to soil nutrient and carbon availability, respiration, and heat production. These correlation patterns were strongly reversed in the conventionally managed soils indicating clear differentiation of microbial functioning related to soil resource availability. Fresh C addition caused proportionally more priming of SOM decomposition (57 vs. 51%) in organically managed soils likely due to mineralization of organic nutrients to satisfy microbial demands during glucose utilization in these more resource deprived soils. The additional heat released from SOM oxidation may explain the similar community level thermodynamic efficiencies between management systems. Restoring fertility to soils with a legacy of nutrient limitation requires a balanced supply of both nutrients and energy to protect stable SOM from microbial degradation. These results highlight the need to consider managing C for the energy it provides to ıcritical biological processes that underpin soil health.
ABSTRACT
Soil is an important source of bacteria and fungi for the plant, but seeds can also provide microbial inocula through heritable or stochastic assembly. Seed-associated microbial communities ...can potentially interact with the host plant through multiple generations. Here, we assessed the impact of two different soil types on the seed microbiome assembly of seven lentil (Lens culinaris) genotypes under environmentally controlled conditions and examined the vertical transmission of bacterial communities from seed to seed across two generations. Bulk soil microbiomes and seed microbiomes were characterized using high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Our results revealed that bacterial communities in the two soils differed significantly and that bacterial communities associated with seeds were significantly impacted by genotype (15%) in one of the soils. Co-occurrence of amplicon sequence variants between generations suggests that members of the genera Cutibacterium, Methylobacterium, Sphingomonas, Streptococcus and Tepidimonas are transmitted and preserved in lentil genotypes irrespective of the soil in which they were grown. Increasing our knowledge of how microbial communities carried by seeds are assembled, transmitted and preserved offers a promising way for future breeding programs to consider microbial communities when selecting for more resilient and productive cultivars.
Assembly of the lentil seed microbiome under different soil types and across multiple generations.
Background
The plant root-rhizosphere microbial community interactions play important roles in crop production as those interactions can be beneficial, detrimental, or neutral for the plant. In
...Brassica napus
, our current understanding of root growth dynamics and dominance of bacterial taxa and their dynamics across growth stages is insufficient. In addition, the association of root traits with dominant and potential growth promoting bacteria across growth stages under field conditions has not been well studied.
Methods
:
Here, we use temporally intensive weekly sampling of
B. napus
over a ten-week period to characterize root growth dynamics, dominant rhizosphere bacterial taxa, and association between the two. We characterized the rhizosphere bacteria using high throughput sequencing of the 16S rRNA genes.
Results
:
B. napus
root length showed distinct growth stage patterns with an increase in root length at early stages followed by s and/or gradual increase at flowering followed by reduction at maturity. Fine root length at the two-three leaf stage and seed yield were significantly positively correlated. The dominant microbial community composition was positively correlated with root traits and environmental variables, with the strongest correlation at the vegetative stage. Positive and significant correlations between individual bacterial genera and root traits were observed during vegetative stage, suggesting possible causal linkage between the two.
Conclusions
The observed significant positive correlations between the bacterial genera and root traits and between root length and seed yield under field conditions suggest the potential for designing root development and beneficial microbial interaction-based canola breeding and management strategies.
Crop rotation is an agronomic practice that is known to enhance productivity and yield, and decrease pest and disease pressure. Economic and other factors have increased the frequency of certain ...crops, including canola, with unknown effects on the below ground microbial communities that impact plant health and performance. This study investigated the effect of 12 years of crop rotation including canola-wheat; canola-pea-barley; and unrotated canola across three geographic sites in Western Canada with diverse soil types and environmental conditions. To provide data on mature, established crop rotation strategies, root exudate profiles, soil nutrient fluxes, and bacterial and fungal microbial community profiles were determined at the flowering stage in the final two (canola) years of the 12-year rotations.
After 12 years of rotation, nutrient fluxes were affected in the soil in an inconsistent manner, with K, NO
, Mg, Ca, P, and Fe fluxes variably impacted by rotation depending on the year and site of sampling. As expected, rotation positively influenced yield and oil content, and decreased disease pressure from Leptosphaeria and Alternaria. In two of the three sites, root exudate profiles were significantly influenced by crop rotation. Bacterial soil, root, and rhizosphere communities were less impacted by crop rotation than the fungal communities. Fungal sequences that were associated with specific rotation strategies were identified in the bulk soil, and included known fungal pathogens in the canola-only strategy. Two closely related fungal sequences identified as Olpidium brassicae were extremely abundant at all sites in both years. One of these sequences was observed uniquely at a single site and was significantly associated with monocropped canola; moreover, its abundance correlated negatively with yield in both years.
Long-term canola monoculture affected root exudate profiles and soil nutrient fluxes differently in the three geographic locations. Bacterial communities were less impacted by rotation compared to the fungal communities, which consistently exhibited changes in composition in all ecological niches at all sites, in both years. Fungal sequences identified as O. brassicae were highly abundant at all sites, one of which was strongly associated with canola monoculture. Soil management decisions should include consideration of the effects on the microbial ecosystems associated with the plants in order to inform best management practices.
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