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78 records · Page 5

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DOE OSTI2021

Colonization of Naive Roots from Populus tremula × alba Involves Successive Waves of Fungi and Bacteria with Different Trophic Abilities

ABSTRACT Through their roots, trees interact with a highly complex community of microorganisms belonging to various trophic guilds and contributing to tree nutrition, development, and protection against stresses. Tree roots select for specific microbial species from the bulk soil communities. The root microbiome formation is a dynamic process, but little is known on how the different microorganisms colonize the roots and how the selection occurs. To decipher whether the final composition of the root microbiome is the product of several waves of colonization by different guilds of microorganisms, we planted sterile rooted cuttings of gray poplar obtained from plantlets propagated in axenic conditions in natural poplar stand soil. We analyzed the root microbiome at different time points between 2 and 50 days of culture by combining high-throughput Illumina MiSeq sequencing of the fungal ribosomal DNA internal transcribed spacer and bacterial 16S rRNA amplicons with confocal laser scanning microscopy observations. The microbial colonization of poplar roots took place in three stages, but bacteria and fungi had different dynamics. Root bacterial communities were clearly different from those in the soil after 2 days of culture. In contrast, if fungi were also already colonizing roots after 2 days, the initial communities were very close to that in the soil and were dominated by saprotrophs. They were slowly replaced by endophytes and ectomycorhizal fungi. The replacement of the most abundant fungal and bacterial community members observed in poplar roots over time suggest potential competition effect between microorganisms and/or a selection by the host. IMPORTANCE The tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development, and protection against different types of stress. They mainly originate from the bulk soil and colonize the root system, which provides a unique nutrient-rich environment for a diverse assemblage of microbial communities. In order to better understand how the tree root microbiome is shaped over time, we observed the composition of root-associated microbial communities of naive plantlets of poplar transferred in natural soil. The composition of the final root microbiome relies on a series of colonization stages characterized by the dominance of different fungal guilds and bacterial community members over time. Our observations suggest an early stabilization of bacterial communities, whereas fungal communities are established following a more gradual pattern.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2001

Microbial contamination of spacecraft

Spacecraft and space habitats supporting human exploration contain a diverse population of microorganisms. Microorganisms may threaten human habitation in many ways that directly or indirectly impact the health, safety, or performance of astronauts. The ability to produce and maintain spacecraft and space stations with environments suitable for human habitation has been established over 40 years of human space flight. An extensive database of environmental microbiological parameters has been provided for short-term (< 20 days) space flight by more than 100 missions aboard the Space Shuttle. The NASA Mir Program provided similar data for long-duration missions. Interestingly, the major bacterial and fungal species found in the Space Shuttle are similar to those encountered in the nearly 15-year-old Mir. Lessons learned from both the US and Russian space programs have been incorporated into the habitability plan for the International Space Station. The focus is on preventive measures developed for spacecraft, cargo, and crews. On-orbit regular housekeeping practices complete with visual inspections are essential, along with microbiological monitoring. Risks associated with extended stays on the Moon or a Mars exploration mission will be much greater than previous experiences because of additional unknown variables. The current knowledge base is insufficient for exploration missions, and research is essential to understand the effects of space flight on biological functions and population dynamics of microorganisms in spacecraft. Equally important is a better understanding of the immune response and of human-microorganism-environment interactions during long-term space habitation.

Mir Project↗

DOE OSTI2022

Phosphate Availability Modulates Root Exudate Composition and Rhizosphere Microbial Community in a Teosinte and a Modern Maize Cultivar

Domestication and breeding have affected interactions between plants and their microbiomes in ways that are only beginning to be understood but may have important implications for recruitment of rhizosphere microorganisms, particularly under stress conditions. We investigated the responses of a modern maize (Zea mays subsp. mays) cultivar and its wild relative, teosinte (Z. mays subsp. parviglumis), to different phosphate availabilities. We appraised responses of the plant-microbial holobiont to phosphate stresses by profiling root exudate metabolomes, and microbial communities in the root endosphere and rhizosphere. We also performed plate assays to quantify phosphate-solubilizing microorganisms from the rhizosphere. Although root exudate metabolite profiles were distinct between the teosinte and modern maize under high phosphate, both plants shifted exudate compositions in response to phosphate stress toward a common metabolite profile. Root and rhizosphere microbial communities also responded significantly to both plant type and the phosphate availability. A subset of bacterial and fungal taxa were differentially abundant under the different phosphate conditions, with each of the three conditions favoring different taxa. Both teosinte and maize rhizospheres harbored phosphate-solubilizing microorganisms under all growth conditions. These results suggest that the root exudation response to phosphate stress was conserved through the domestication of maize from teosinte, shifting exudation levels of specific metabolites. Although microbial communities also shifted, plate-based assays did not detect selective recruitment of phosphate solubilizers in response to phosphate availability.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Signatures of prescribed fire in the microbial communities of Cornus florida are largely undetectable five months post-fire

Prescribed burn is a management tool that influences the physical structure and composition of forest plant communities and their associated microorganisms. Plant-associated microorganisms aid in host plant disease tolerance and increase nutrient availability. The effects of prescribed burn on microorganisms associated with native ecologically and economically important tree species, such as Cornus florida L. (flowering dogwood), are not well understood, particularly in aboveground plant tissues (e.g., leaf, stem, and bark tissues). The objective of this study was to use 16S rRNA gene and ITS2 region sequencing to evaluate changes in bacterial and fungal communities of five different flowering dogwood-associated niches (soil, roots, bark, stem, and leaves) five months following a prescribed burn treatment. The alpha- and beta-diversity of root bacterial/archaeal communities differed significantly between prescribed burn and unburned control-treated trees. In these bacterial/archaeal root communities, we also detected a significantly higher relative abundance of sequences identified as Acidothermaceae, a family of thermophilic bacteria. No significant differences were detected between prescribed burn-treated and unburned control trees in bulk soils or bark, stem, or leaf tissues. The findings of our study suggest that prescribed burn does not significantly alter the aboveground plant-associated microbial communities of flowering dogwood trees five months following the prescribed burn application. Further studies are required to better understand the short- and long-term effects of prescribed burns on the microbial communities of forest trees.

16S rRNA↗

DOE OSTI2023

The effects of mixed-species root zones on the resistance of soil bacteria and fungi to long-term experimental and natural reductions in soil moisture

Mixed forest stands tend to be more resistant to drought than species-specific stands partially due to complementarity in root ecology and physiology. For this work, we asked whether complementary differences in the drought resistance of soil microbiomes might contribute to this phenomenon. We experimented on the effects of reduced soil moisture on bacterial and fungal community composition in species-specific (single species) and mixed-species root zones of Norway spruce and European beech forests in a 5-year-old throughfall-exclusion experiment and across seasonal (spring-summer-fall) and latitudinal moisture gradients. Bacteria were most responsive to changes in soil moisture, especially members of Rhizobiales, while fungi were largely unaffected, including ectomycorrhizal fungi (EMF). Community resistance was higher in spruce relative to beech root zones, corresponding with the proportions of drought-favored (more in spruce) and drought-sensitive bacterial taxa (more in beech). The spruce soil microbiome also exhibited greater resistance to seasonal changes between spring (wettest) and fall (driest). Mixed-species root zones contained a hybrid of beech- and spruce-associated microbiomes. Several bacterial populations exhibited either enhanced resistance or greater susceptibility to drought in mixed root zones. Overall, patterns in the relative abundances of soil bacteria closely tracked moisture in seasonal and latitudinal precipitation gradients and were more predictive of soil water content than other environmental variables. We conclude that complementary differences in the drought resistance of soil microbiomes can occur and the likeliest form of complementarity in mixed-root zones coincides with the enrichment of drought-tolerant bacteria associated with spruce and the sustenance of EMF by beech.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Plant root associated chitinases: structures and functions

Chitinases degrade chitin, a linear homopolymer of β-1,4-linked N-acetyl-D-glucosamine (GlcNAc) residues found in the cell walls of fungi and the exoskeletons of arthropods. They are secreted by the roots into the rhizosphere, a complex and dynamic environment where intense nutrient exchange occurs between plants and microbes. Here we modeled, expressed, purified, and characterized Zea mays and Oryza sativa root chitinases, and the chitinase of a symbiotic bacterium, Chitinophaga oryzae 1303 for their activities with chitin, di-, tri-, and tetra-saccharides and Aspergillus niger, with the goal of determining their role(s) in the rhizosphere and better understanding the molecular mechanisms underlying plant-microbe interactions. We show that Zea mays basic endochitinase (ZmChi19A) and Oryza sativa chitinase (OsChi19A) are from the GH19 chitinase family. The Chitinophaga oryzae 1303 chitinase (CspCh18A) belongs to the GH18 family. The three enzymes have similar apparent K M values of (20-40 µM) for the substrate 4-MU-GlcNAc 3 . They vary in their pH and temperature optima with OsChi19A activity optimal between pH 5–7 and 30–40°C while ZmChi19A and CspCh18A activities were optimal at pH 7-9 and 50–60°C. Modeling and site-directed mutation of ZmChi19A identified the catalytic cleft and the active residues E147 and E169 strategically positioned at ~8.6Å from each other in the folded protein. Cleavage of 4-MU-GlcNAc 3 was unaffected by the absence of the CBD but diminished in the absence of the flexible C-terminal domain. However, unlike for the soluble substrate, the CBD and the newly identified flexible C-terminal domain were vital for inhibiting Aspergillus niger growth. The results are consistent with the involvement of the plant chitinases in defense against pathogens like fungi that have chitin exoskeletons. In summary, we have characterized the functional features and structural domains necessary for the activity of two plant root chitinases that are believed to be involved in plant defense and a bacterial chitinase that, along with the plant chitinases, may participate in nutrient recycling in the rhizosphere.

60 APPLIED LIFE SCIENCES↗