Soil microorganisms found in the root zone impact plant growth and development, but the potential to harness these benefits is hampered by the sheer abundance and diversity of the players influencing desirable plant traits. Here, we report a high level of reproducibility of soil microbiomes in altering plant flowering time and soil functions when partnered within and between plant hosts. We used a multi-generation experimental system using Arabidopsis thaliana Col to select for soil microbiomes inducing earlier or later flowering times of their hosts. We then inoculated the selected microbiomes from the tenth generation of plantings into the soils of three additional A. thaliana genotypes (Ler, Be, RLD) and a related crucifer (Brassica rapa). With the exception of Ler, all other plant hosts showed a shift in flowering time corresponding with the inoculation of early- or late-flowering microbiomes. Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment. Plant hosts grown with the late-flowering-associated microbiomes showed consequent increases in inflorescence biomass for three A. thaliana genotypes and an increase in total biomass for B. rapa. The increase in biomass was correlated with two- to five-fold enhancement of microbial extracellular enzyme activities associated with nitrogen mineralization in soils. The reproducibility of the flowering phenotype across plant hosts suggests that microbiomes can be selected to modify plant traits and coordinate changes in soil resource pools.

We show that choice of soil microbiome transfer method, i.e. direct soil transfers and a common soil wash procedure, dramatically influences the microbiome that develops in a new environment, using high-throughput amplicon sequencing of 16S rRNA genes and the fungal internal transcribed spacer (ITS) region. After 3 weeks of incubation in commercial potting mix, microbiomes were most similar to the source soil when a greater volume of initial soil was transferred (5% v/v transfer), and least similar when using a soil wash. Abundant operational taxonomic units were substantially affected by transfer method, suggesting that compounds transferred from the source soil, shifts in biotic interactions, or both, play an important role in their success.

Plant rhizospheres encompass a dynamic zone of interactions between microorganisms and their respective plant hosts. For decades, researchers have worked to understand how these complex interactions influence different aspects of plant growth, development, and evolution. Studies of plant-microbial interactions in the root zone have typically focused on the effect of single microbial species or strains on a plant host. These studies, however, provide only a snapshot of the complex interactions that occur in the rhizosphere, leaving researchers with a limited understanding of how the complex microbiome influences the biology of the plant host. To better understand how rhizosphere interactions influence plant growth and development, novel frameworks and research methodologies could be implemented. In this perspective, we propose applying concepts in evolutionary biology to microbiome experiments for improved understanding of group-to-group and community-level microbial interactions influencing soil nutrient cycling. We also put forth simple experimental designs utilizing -omics techniques that can reveal important changes in the rhizosphere impacting the plant host. A greater focus on the components of complexity of the microbiome and how these impact plant host biology could yield more insight into previously unexplored aspects of host-microbe biology relevant to crop production and protection.

The microbiome of a vineyard may play a critical role in fruit development, and consequently, may impact quality properties of grape and wine. Vineyard management approaches that have directly manipulated the microbiome of grape clusters have been studied, but little is known about how vineyard management practices that impact the soil microbial pool can influence this dynamic. We examined three under-vine soil management practices: 1) herbicide application, 2) soil cultivation (vegetation removal), and 3) natural vegetation (no vegetation removal) in a Riesling vineyard in New York over a three-year period. The microbiomes associated with soil and grapes were profiled using high-throughput sequencing of the bacterial 16 S rRNA gene and fungal ITS regions. Our results showed that soil bacterial composition under natural vegetation differs from that seen in glyphosate-maintained bare soil. Soil fungal composition under the natural vegetation treatment was distinct from other treatments. Although our study revealed soil microbiome shifts based on under-vine management, there were no corresponding changes in fruit-associated microbial composition. These results suggested that other vineyard management practices or environmental factors are more influential in shaping the grape-associated microbiome.

Urban grasslands are turfgrass dominated landscapes of varying functions and uses that are ubiquitous in areas associated with human population growth and urbanization. While these landscapes are perceived to serve a primarily aesthetic function, they provide a multitude of beneficial ecosystem functions that impervious surfaces do not provide. Urban grassland soils have been shown to accumulate carbon (C) and nitrogen (N) for decades, matching native grasslands and eastern hardwood forest soils in terms of C and N densities. The establishment and maintenance of urban grasslands alters many microbially-mediated biogeochemical processes in soils, including soil organic matter (SOM) dynamics. Despite strong evidence of alterations to soil C and N cycling, the impacts of maintaining urban grasslands on soil microbiomes and their functions remain understudied compared to other ecosystems. Typical management practices can directly and indirectly affect edaphic factors in urban grasslands, which in turn, could impact soil processes mediated by microorganisms. We reviewed the existing literature on urban grassland management, focusing on how mowing, fertilization, irrigation, grass species composition, and soil cultivation could impact the composition and function of soil microorganisms. Although sparse, the literature indicates that the techniques used to maintain urban grassland habitats broadly select for copiotrophic microorganisms adapted to higher resource availability. Additionally, the studies indicate that greater soil fertility and plant productivity found in urban grasslands facilitate the accumulation of soil C and N, as well as SOM as compared to other land-use types. However, effects on soil biology and biogeochemistry depend on specific management practices, which are quite variable. Future research on soil C and N dynamics in urban grasslands should focus on the dominant component of this ecosystem—residential lawns—however, much of the existing scientific literature featuring turfgrass systems focus heavily on golf courses, athletic fields, and major tourist parks.

The consequences of climate change urgently demand the reduction of atmospheric carbon, including by sequestering carbon in soil. The glomalin-related soil proteins (GRSP) of arbuscular mycorrhizal fungi (AMF) are renowned for their soil aggregation and carbon sequestration properties. With their considerable binding abilities, GRSP can also adsorb various cations and sequester heavy metals in soil, thereby assisting in soil fertilization and remediation efforts. However, despite its benefits for soil health and climate change, the mechanisms underlying these traits in the context of soil chemistry remain unexplored. In this review, we focus on three crucial roles of GRSP—long-term carbon sequestration, soil aggregation, and soil remediation and fertility—in the context of the chemical characteristics elucidated by previous research, namely hydrophobicity, amid group glycosylation (N-glycosylation), and metal adsorption. Based on the proposed chemical mechanisms, the current review also offers insight into soil factors that may influence the persistence of GRSP. We conclude by proposing a working model for GRSP, aiming to establish a conceptual platform for future research to examine GRSP in terms of their known or novel chemical and biochemical reactions, thereby improving our understanding of this important group of soil proteins.