Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil

Howe, Adina; Yang, Fan; Williams, Ryan J.; Meyer, Folker; Hofmockel, Kirsten

doi:10.1371/journal.pone.0166578

Cited by 17 publications

(10 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…29 Additionally, many of these CAZymes were assigned to Bacteroidetes , Firmicutes , Chloroflexi , and Spirochaetes , which are important contributors to the degradation of lignocellulosic material in various environments. 61–64 Planctomycetes and Euryarchaeota were also detected in the presence of HAs and have been associated with cellulose decomposition with GTs, 65,66 and metabolism of carbohydrates with GHs, 42,63 respectively.…”

Section: Resultsmentioning

confidence: 99%

Dual Role of Humic Substances As Electron Donor and Shuttle for Dissimilatory Iron Reduction

Stern

Mejia

et al. 2018

Environ. Sci. Technol.

144

View full text Add to dashboard Cite

Dissimilatory iron-reducing bacteria (DIRB) are known to use humic substances (HS) as electron shuttles for dissimilatory iron reduction (DIR) by transferring electrons to HS-quinone moieties, which in turn rapidly reduce Fe(III) oxides. However, the potential for HS to serve as a source of organic carbon (OC) that can donate electrons for DIR is unknown. We studied whether humic acids (HA) and humins (HM) recovered from peat soil by sodium pyrophosphate extraction could serve as both electron shuttles and electron donors for DIR by freshwater sediment microorganisms. Both HA and HM served as electron shuttles in cultures amended with glucose. However, only HA served as an electron donor for DIR. Metagenomes from HA-containing cultures had an overrepresentation of genes involved in polysaccharide and to a lesser extent aromatic compound degradation, suggesting complex OC metabolism. Genomic searches for the porin-cytochrome complex involved in DIR resulted in matches to Ignavibacterium/Melioribacter, DIRB capable of polymeric OC metabolism. These results indicate that such taxa may have played a role in both DIR and decomposition of complex OC. Our results suggest that decomposition of HS coupled to DIR and other anaerobic pathways could play an important role in soil and sediment OC metabolism.

show abstract

Section: Resultsmentioning

confidence: 99%

Dual Role of Humic Substances As Electron Donor and Shuttle for Dissimilatory Iron Reduction

Stern

Mejia

et al. 2018

Environ. Sci. Technol.

144

View full text Add to dashboard Cite

show abstract

“…While the majority of Gammaproteobacteria enrichment was due to Pseudomonas OTUs not found in the soil controls, the other trends are less easily explained. Firmicutes and Actinobacteria are associated with carbon cycling processes in fertilized prairie soils (40), which could explain their prevalence in polysaccharide modules. In addition, Firmicutes were prevalent in anaerobic and heat stress modules.…”

Section: Discussionmentioning

confidence: 99%

Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules

Naylor

Fansler

Brislawn

et al. 2020

mBio

Self Cite

View full text Add to dashboard Cite

ABSTRACT The soil microbiome represents one of the most complex microbial communities on the planet, encompassing thousands of taxa and metabolic pathways, rendering holistic analyses computationally intensive and difficult. Here, we developed an alternative approach in which the complex soil microbiome was broken into components (“functional modules”), based on metabolic capacities, for individual characterization. We hypothesized that reproducible, low-complexity communities that represent functional modules could be obtained through targeted enrichments and that, in combination, they would encompass a large extent of the soil microbiome diversity. Enrichments were performed on a starting soil inoculum with defined media based on specific carbon substrates, antibiotics, alternative electron acceptors under anaerobic conditions, or alternative growing conditions reflective of common field stresses. The resultant communities were evaluated through 16S rRNA amplicon sequencing. Less permissive modules (anaerobic conditions, complex polysaccharides, and certain stresses) resulted in more distinct community profiles with higher richness and more variability between replicates, whereas modules with simple substrates were dominated by fewer species and were more reproducible. Collectively, approximately 27% of unique taxa present in the liquid soil extract control were found across functional modules. Taxa that were underrepresented or undetected in the source soil were also enriched across the modules. Metatranscriptomic analyses were carried out on a subset of the modules to investigate differences in functional gene expression. These results demonstrate that by dissecting the soil microbiome into discrete components it is possible to obtain a more comprehensive view of the soil microbiome and its biochemical potential than would be possible using more holistic analyses. IMPORTANCE The taxonomic and functional diversity inherent to the soil microbiome complicate assessments of the metabolic potential carried out by the community members. An alternative approach is to break down the soil microbiome into reduced-complexity subsets based on metabolic capacities (functional modules) prior to sequencing and analysis. Here, we demonstrate that this approach successfully identified specific phylogenetic and biochemical traits of the soil microbiome that otherwise remained hidden from a more top-down analysis.

show abstract

“…Efforts are currently being made to characterize and identify microbial functional genes across environmental slopes to know their contributions to ecological services (Howe et al 2016;Glick 2012). Previously, Nithyatharani and Kavitha (2018) reported the presence of some PGPB and their nifH genes in termite mound soils.…”

Section: Introductionmentioning

confidence: 99%

Unveiling Plant-Beneficial Function as Seen in Bacteria Genes from Termite Mound Soil

Enagbonma

Babalola

2020

J Soil Sci Plant Nutr

View full text Add to dashboard Cite

The use of termite mound soils in enhancing soil fertility and plant growth, especially in areas with poor soil conditions, has been recommended by many research studies. Most of these recommendations are, however, based on the high nutrient levels in termite mound soils. Thus, this study aimed to verify if plant growth-promoting bacteria in termite soils also play a role in improving plant growth. To achieve our purpose, we made an effort in characterizing the bacterial genes contributing to plantbeneficial function in termite mound soils with the shotgun metagenomics method. Results from this study revealed the presence of bacterial genes involved in the production of siderophores, acetoin, trehalose, phenazine, butanediol, 4-hydroxybenzoate, chitinase, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, quorum sensing molecules, and mineral phosphate solubilization. In addition, we identified bacterial genes involved in the manufacturing of catalases, peroxidases, and superoxide dismutases that confer resistance to oxidative stresses in plants. Bacterial genes responsible for glycine-betaine production and cold and heat shock tolerance which helps in withstanding abiotic stress, were also present. With these plant growth-promoting traits observed in bacteria from termite mound soils, we recommend the isolation and the use of termite mound soil bacteria both in greenhouse and field trials to further ascertain their potential in improving soil fertility and crop production.

show abstract

Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil

Cited by 17 publications

References 51 publications

Dual Role of Humic Substances As Electron Donor and Shuttle for Dissimilatory Iron Reduction

Dual Role of Humic Substances As Electron Donor and Shuttle for Dissimilatory Iron Reduction

Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules

Unveiling Plant-Beneficial Function as Seen in Bacteria Genes from Termite Mound Soil

Contact Info

Product

Resources

About