Microbial communities and diazotrophic activity differ in the root‐zone of Alamo and Dacotah switchgrass feedstocks

Rodrigues, Richard R.; Moon, Jin-Young; Zhao, Bingyu; Williams, Mark A.

doi:10.1111/gcbb.12396

Cited by 26 publications

(29 citation statements)

References 100 publications

(113 reference statements)

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“…Host-microbe associations are heritable (Peiffer et al, 2013), and this variation can be used to identify and select genotypes with superior abilities to benefit from these associations from an agronomic viewpoint (Lima et al, 1987;Urquiaga et al, 1992;Dong et al, 2018). There is some evidence for genetic or ecotypic variability in host-microbe nutrient dynamics within switchgrass, supporting a hypothesis that high-biomass cultivars will be better able to support a bacterial community with high nitrogenase activity compared with low-biomass cultivars (Rodrigues et al, 2017).…”

Section: Nitrogen: To Fertilize or Notmentioning

confidence: 99%

Soil Quality and Region Influence Performance and Ranking of Switchgrass Genotypes

et al. 2019

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Development of switchgrass (Panicum virgatum L.) as a dedicated bioenergy feedstock requires intensive and extensive breeding programs that include careful and thoughtful consideration of appropriate target populations of environments (TPEs). The purpose of this study was to evaluate region (climate), soil quality, and N fertilization level as potential factors influencing the choice of TPE. A total of 45 switchgrass genotypes were evaluated in uniform field studies at six field sites defined as prime or marginal soils in New Jersey, South Dakota, and Wisconsin. Region and soil quality had strong interactions with genotype, but N fertilization had little impact on genetic variation or ranking of genotypes. Lowland genotypes were considerably more sensitive than upland genotypes to interactions with environmental factors, probably due to these field sites being outside of the traditional lowland adaptation zones. Genotype rankings were highly inconsistent across regions and soil types, indicating that breeding programs that target marginal soils should be located on soils that represent the appropriate TPE. Furthermore, interactions across the three regions suggest that breeding programs for the lowland ecotype should be subdivided into different sets of TPEs, which are largely a function of hardiness zone and annual precipitation. Lastly, even with negligible interactions involving N fertilization level, future definitions of TPEs should be based on minimal or no N fertilizer applications to allow breeders to select plants with greater N‐use efficiency, N‐scavenging ability, and N‐recycling efficiency.

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Section: Nitrogen: To Fertilize or Notmentioning

confidence: 99%

Soil Quality and Region Influence Performance and Ranking of Switchgrass Genotypes

et al. 2019

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“…Diazotrophs have been identified in high abundance and diversity in association in the rhizosphere of gramineous C3 and C4 crops such as wheat, maize, rice, sugarcane as well as in many perennial grass species (Roper and Gupta 2016). Diazotrophic community size and composition was found to vary among plant species and plant varieties, including maize (Rodriguez-Blanco et al 2015), sorghum (Coelho et al 2009), switchgrass (Rodrigues et al 2017), and rice (Engelhard et al 2000, Knauth et al 2005.…”

Section: Biological Nutrient Acquisitionmentioning

confidence: 99%

A preview of perennial grain agriculture: knowledge gain from biotic interactions in natural and agricultural ecosystems

et al. 2017

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Abstract. Compared to their annual analogues, perennial grain cropping systems provide various beneficial attributes for the environment and ecosystem services related to resource use efficiency, soil erosion, and soil conservation. However, there is only limited understanding of the multiple biotic interactions in perennial cropping systems and their potential effects on the crop, involving plant growth-promoting and pathogenic microorganisms, beneficial and detrimental faunal organisms below-and above-ground, weeds, and overall biodiversity effects. We use information from studies carried out in managed and natural perennial systems of analogous structure such as perennial energy crop production systems and grasslands to highlight and specify biotic interactions and processes, which potentially constitute advantages and constraints in developing perennial grain cropping systems. Concerning the relevance of soil microorganisms and potential perennial crop breeding goals, we focus on a range of plant-microbe interactions in the rhizosphere involved in biofertilization, phytostimulation, and biological control of soil pathogens. We consider relationships within the faunal community emphasizing arthropod pests and their natural enemies, as well as crop-weed interactions. Based on these outcomes and in comparison with annual systems, we discuss and compile benefits, options, and limitations of management of crop-associated biotic interactions and biodiversity, which might contribute to reproducible and sustainable effects of perennial grain crop productivity. We conclude that management strategies for perennial grain cropping systems depend much more on ecological processes and interactions operating in natural ecosystems than those in annual cropping systems. Consequently, the use of agrochemicals for pest, weed, and disease control, as well as the use of synthetic fertilizers, counteracts the principle functions of the system and would strongly degrade the potential of biotic benefits. We also found that there is only vague information on the long-term productivity and cultivation period of perennial grain crops, the specific management operations of replacement, and the potential development and management of weed and pest populations. Overall, an advanced understanding of interactions between the crop and its biotic environment provides the opportunity to manipulate specific functional traits of crop-associated organisms for improved management and crop productivity, but significant research challenges for implementation of perennial grain crops still remain.

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“…For the Rodrigues 2017 dataset, the OTU table was obtained from previously performed analysis (Rodrigues et al, 2017). 104…”

Section: Sequence Data Analysis and Picking Of Operational Taxonomic mentioning

confidence: 99%

“…A diverse set of data composed of 61 samples from two different published datasets and collected from multiple locations 83 (Jesus et al, 2016;Rodrigues et al, 2016) were used for this study. Data were obtained from the NCBI and selected 84 based on the availability of the raw (16S rRNA) sequence data of root-zone bacteria from switchgrass and that for an out-85 group of reference (native and/or other grasses) plants.…”

Section: Datasets Used In the Study 82mentioning

confidence: 99%

COREMIC: a web-tool to search for a root-zone associated CORE MICrobiome

et al. 2017

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17Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding 18 how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains 19 only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can 20 be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the bur-21 geoning growth of information from databases, our tool "COREMIC" meets a great need in the search for understanding 22 niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly 23 statistically robust web-tool (http://coremic2.appspot.com), developed using Google App Engine, to help in the process 24 of database mining to identify the "core microbiome" associated with a given habitat. A case study is presented using 25 data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The 26 methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass 27 microbiome. Even across a diverse set of soils (5 environments), and conservative statistical criteria (presence in more 28 than 90% samples and FDR q-val < 0.05% for Fisher's exact test) a core set of bacteria associated with switchgrass was 29 . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/147009 doi: bioRxiv preprint first posted online Jun. 7, 2017; R. Rodrigues et al. 2observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and 30 Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal 31 antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that 32 shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case 33 study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using cur-34 rently available databases and a unique freely available software. 35 36

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Microbial communities and diazotrophic activity differ in the root‐zone of Alamo and Dacotah switchgrass feedstocks

Cited by 26 publications

References 100 publications

Soil Quality and Region Influence Performance and Ranking of Switchgrass Genotypes

Soil Quality and Region Influence Performance and Ranking of Switchgrass Genotypes

A preview of perennial grain agriculture: knowledge gain from biotic interactions in natural and agricultural ecosystems

COREMIC: a web-tool to search for a root-zone associated CORE MICrobiome

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