Switchgrass (Panicum virgatum L.) remains the preeminent American perennial (C4) bioenergy crop for cellulosic ethanol that could help displace over a quarter of the US current petroleum consumption. Intriguingly, there is often little response to nitrogen fertilizer once stands are established. The rhizosphere microbiome plays a critical role in nitrogen cycling and overall plant nutrient uptake. We used high-throughput metagenomic sequencing to characterize the switchgrass rhizosphere microbial community (5.37 billion Illumina reads at 805 Gbp of data) before and after a nitrogen fertilization event for established stands on marginal land. We examined community structure, bulk metabolic potential, and resolved 29 individual bacteria genomes via metagenomic de novo assembly. Community structure and diversity were not significantly different before and after fertilization; however, the bulk metabolic potential of carbohydrate-active enzymes was depleted after fertilization. We resolved 29 metagenomic assembled genomes including some from the ‘most wanted’ soil taxa such as Verrucomicrobia, Candidate phyla UBA10199, Acidobacteria (rare subgroup 23), Dormibacterota, and the very rare Candidatus Eisenbacteria. The Dormibacterota (formally candidate division AD3) we identified have the potential for autotrophic CO utilization, which may impact carbon partitioning and storage. Our study also suggests that the rhizosphere microbiome may be involved in providing associative nitrogen fixation (ANF) via the novel diazotroph Janthinobacterium, which may partially explain why switchgrass growth is insensitive to fertilizer.

Animals form functional units with their microbial communities, termed metaorganisms. While extensive research has been conducted on a few model animals, much remains unknown about the microbial diversity in most species. Here, we describe the taxonomic profile of the microbes from the outer gut mucus layer from the Northeast Arctic cod or also called the migrating Atlantic cod using a shotgun DNA sequencing approach. We provide metagenomes from six individuals. The results reveal three different taxonomic profile “types": Type I is dominated in numbers by Pseudomonaceae (44%) and Xanthomonadaceae (13%), Type II contains 65% Vibrionaceae and Type III contains 76% Enterobacteriaceae. This stands in sharp contrast to the bacterial diversity of the transient gut content (i.e., feces). Additionally, binning of assembled reads followed by phylogenomic analyses place a high-completeness bin of Type I within the Pseudomonas fluorescens group, one bin of Type II within the Photobacterium phosphoreum clade, and finally a bin of Type III within the Escherichia/Shigella group. In conclusion, we describe the adherent bacterial diversity in the Northeast Arctic cod's intestine using shotgun sequencing, revealing different taxonomic profiles compared to the more homogenous transient (fecal) microbiota. This suggests that the intestine contains two separate and distinct microbial populations.