skip to main content

This content will become publicly available on April 12, 2023

Title: Temporally Selective Modification of the Tomato Rhizosphere and Root Microbiome by Volcanic Ash Fertilizer Containing Micronutrients
ABSTRACT Food crops are grown with fertilizers containing nitrogen, phosphorus, and potassium (macronutrients) along with magnesium, calcium, boron, and zinc (micronutrients) at different ratios during their cultivation. Soil and plant-associated microbes have been implicated to promote plant growth, stress tolerance, and productivity. However, the high degree of variability across agricultural environments makes it difficult to assess the possible influences of nutrient fertilizers on these microbial communities. Uncovering the underlying mechanisms could lead us to achieve consistently improved food quality and productivity with minimal environmental impacts. For this purpose, we tested a commercially available fertilizer (surface-mined volcanic ash deposit Azomite) applied as a supplement to the normal fertilizer program of greenhouse-grown tomato plants. Because this treatment showed a significant increase in fruit production at measured intervals, we examined its impact on the composition of below-ground microbial communities, focusing on members identified as “core taxa” that were enriched in the rhizosphere and root endosphere compared to bulk soil and appeared above their predicted neutral distribution levels in control and treated samples. This analysis revealed that Azomite had little effect on microbial composition overall, but it had a significant, temporally selective influence on the core taxa. Changes in the composition of the core more » taxa were correlated with computationally inferred changes in functional pathway enrichment associated with carbohydrate metabolism, suggesting a shift in available microbial nutrients within the roots. This finding exemplifies how the nutrient environment can specifically alter the functional capacity of root-associated bacterial taxa, with the potential to improve crop productivity. IMPORTANCE Various types of soil fertilizers are used routinely to increase crop yields globally. The effects of these treatments are assessed mainly by the benefits they provide in increased crop productivity. There exists a gap in our understanding of how soil fertilizers act on the plant-associated microbial communities. The underlying mechanisms of nutrient uptake are widely complex and, thus, difficult to evaluate fully but have critical influences on both soil and plant health. Here, we presented a systematic approach to analyzing the effects of fertilizer on core microbial communities in soil and plants, leading to predictable outcomes that can be empirically tested and used to develop simple and affordable field tests. The methods described here can be used for any fertilizer and crop system. Continued effort in advancing our understanding of how fertilizers affect plant and microbe relations is needed to advance scientific understanding and help growers make better-informed decisions. « less
Authors:
; ; ; ;
Editors:
Semrau, Jeremy D.
Award ID(s):
1838299
Publication Date:
NSF-PAR ID:
10331762
Journal Name:
Applied and Environmental Microbiology
Volume:
88
Issue:
7
ISSN:
0099-2240
Sponsoring Org:
National Science Foundation
More Like this
  1. Campbell, Barbara J. (Ed.)
    ABSTRACT In nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return, plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast-growing copiotrophs, slow-growing oligotrophs) and plant (C 3 forb, C 4 grass) communities residing in a nutrient-poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized versus unfertilized) and plant association (bulk versus rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass versus forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease-suppressive bacterial taxa, and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilizationmore »serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling. IMPORTANCE Over the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorus deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline, and the abundance of copiotrophic taxa is anticipated to increase in bacterial communities. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter diversity and metabolism of rhizosphere bacterial communities in unexpected ways.« less
  2. Semrau, Jeremy D. (Ed.)
    ABSTRACT This study investigated the differences in microbial community abundance, composition, and diversity throughout the depth profiles in soils collected from corn and soybean fields in Iowa (United States) using 16S rRNA amplicon sequencing. The results revealed decreased richness and diversity in microbial communities at increasing soil depth. Soil microbial community composition differed due to crop type only in the top 60 cm and due to location only in the top 90 cm. While the relative abundance of most phyla decreased in deep soils, the relative abundance of the phylum Proteobacteria increased and dominated agricultural soils below the depth of 90 cm. Although soil depth was the most important factor shaping microbial communities, edaphic factors, including soil organic matter, soil bulk density, and the length of time that deep soils were saturated with water, were all significant factors explaining the variation in soil microbial community composition. Soil organic matter showed the highest correlation with the exponential decrease in bacterial abundance with depth. A greater understanding of how soil depth influences the diversity and composition of soil microbial communities is vital for guiding sampling approaches in agricultural soils where plant roots extend beyond the upper soil profile. In the long term, a greater knowledgemore »of the influence of depth on microbial communities should contribute to new strategies that enhance the sustainability of soil, which is a precious resource for food security. IMPORTANCE Determining how microbial properties change across different soils and within the soil depth profile will be potentially beneficial to understanding the long-term processes that are involved in the health of agricultural ecosystems. Most literature on soil microbes has been restricted to the easily accessible surface soils. However, deep soils are important in soil formation, carbon sequestration, and providing nutrients and water for plants. In the most productive agricultural systems in the United States where soybean and corn are grown, crop plant roots extend into the deeper regions of soils (>100 cm), but little is known about the taxonomic diversity or the factors that shape deep-soil microbial communities. The findings reported here highlight the importance of soil depth in shaping microbial communities, provide new information about edaphic factors that influence the deep-soil communities, and reveal more detailed information on taxa that exist in deep agricultural soils.« less
  3. Investigations of plant-soil feedbacks (PSF) and plant-microbe interactions often rely exclusively on greenhouse experiments, yet we have little understanding of how, and when, results can be extrapolated to explain phenomena in nature. A systematic comparison of microbial communities using the same host species across study environments can inform the generalizability of such experiments. We used Illumina MiSeq sequencing to characterize the root-associated fungi of two foundation grasses from a greenhouse PSF experiment, a field PSF experiment, field monoculture stands, and naturally occurring resident plants in the field. A core community consisting < 10% of total fungal OTU richness but > 50% of total sequence abundance occurred in plants from all study types, demonstrating the ability of field and greenhouse experiments to capture the dominant component of natural communities. Fungal communities were plant species-specific across the study types, with the core community showing stronger host specificity than peripheral taxa. Roots from the greenhouse and field PSF experiments had lower among sample variability in community composition and higher diversity than those from naturally occurring, or planted monoculture plants from the field. Core and total fungal composition differed substantially across study types, and dissimilarity between fungal communities did not predict plant-soil feedbacks measured in experiments.more »These results suggest that rhizobiome assembly mechanisms in nature differ from the dynamics of short-term, inoculation studies. Our results validate the efficacy of common PSF experiment designs to test soil inoculum effects, and highlight the challenges of scaling the underlying microbial mechanisms of plant responses from whole-community inoculation experiments to natural ecosystems.« less
  4. Liu, Shuang-Jiang (Ed.)
    ABSTRACT Root-associated microbes are key players in plant health, disease resistance, and nitrogen (N) use efficiency. It remains largely unclear how the interplay of biological and environmental factors affects rhizobiome dynamics in agricultural systems. In this study, we quantified the composition of rhizosphere and bulk soil microbial communities associated with maize ( Zea mays L.) and soybean ( Glycine max L.) in a long-term crop rotation study under conventional fertilization and low-N regimes. Over two growing seasons, we evaluated the effects of environmental conditions and several treatment factors on the abundance of rhizosphere- and soil-colonizing microbial taxa. Time of sampling, host plant species, and N fertilization had major effects on microbiomes, while no effect of crop rotation was observed. Using variance partitioning as well as 16S sequence information, we further defined a set of 82 microbial genera and functional taxonomic groups at the subgenus level that show distinct responses to treatment factors. We identified taxa that are highly specific to either maize or soybean rhizospheres, as well as taxa that are sensitive to N fertilization in plant rhizospheres and bulk soil. This study provides insights to harness the full potential of soil microbes in maize and soybean agricultural systems throughmore »plant breeding and field management. IMPORTANCE Plant roots are colonized by large numbers of microbes, some of which may help the plant acquire nutrients and fight diseases. Our study contributes to a better understanding of root-colonizing microbes in the widespread and economically important maize-soybean crop rotation system. The long-term goal of this research is to optimize crop plant varieties and field management to create the best possible conditions for beneficial plant-microbe interactions to occur. These beneficial microbes may be harnessed to sustainably reduce dependency on pesticides and industrial fertilizer. We identify groups of microbes specific to the maize or to the soybean host and microbes that are sensitive to nitrogen fertilization. These microbes represent candidates that may be influenced through plant breeding or field management, and future research will be directed toward elucidating their roles in plant health and nitrogen usage.« less
  5. Abstract
    Excessive phosphorus (P) applications to croplands can contribute to eutrophication of surface waters through surface runoff and subsurface (leaching) losses. We analyzed leaching losses of total dissolved P (TDP) from no-till corn, hybrid poplar (Populus nigra X P. maximowiczii), switchgrass (Panicum virgatum), miscanthus (Miscanthus giganteus), native grasses, and restored prairie, all planted in 2008 on former cropland in Michigan, USA. All crops except corn (13 kg P ha−1 year−1) were grown without P fertilization. Biomass was harvested at the end of each growing season except for poplar. Soil water at 1.2 m depth was sampled weekly to biweekly for TDP determination during March–November 2009–2016 using tension lysimeters. Soil test P (0–25 cm depth) was measured every autumn. Soil water TDP concentrations were usually below levels where eutrophication of surface waters is frequently observed (&gt; 0.02 mg L−1) but often higher than in deep groundwater or nearby streams and lakes. Rates of P leaching, estimated from measured concentrations and modeled drainage, did not differ statistically among cropping systems across years; 7-year cropping system means ranged from 0.035 to 0.072 kg P ha−1 year−1 with large interannual variation. Leached P was positively related to STP, which decreased over the 7 years in all systems. These results indicate that both P-fertilized and unfertilized cropping systems mayMore>>