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Abstract: In the legume-rhizobia mutualism, symbiotic success changes with time, complicating early strain quality evaluations. We measured host biomass at three and six months after inoculation of bearded clover (Trifolium barbigerum) with 77 strains of Rhizobium leguminosarum. Across timepoints, strain performance rankings based on host biomass varied: some top strains at three months later declined, whereas initially low-ranking strains ultimately surpassed them. This suggests biological tradeoffs in the timing of nitrogen fixation and the allocation of the host resources. Our results highlight that symbiont function can vary over time and that single timepoint data collection risks inaccurately identifying long-term beneficial strains. 

Legumes (Fabaceae) have developed a symbiotic relationship with nitrogen-fixing bacteria called rhizobia to meet their nitrogen needs. Legumes recruit rhizobia from the soil, house them in root organs called nodules, and manipulate bacterial metabolism, providing carbon and receiving bacterially fixed nitrogen in return. One mechanism of host control is through a family of antimicrobial peptides that only appears in the inverted repeat lacking clade (IRLC) of the legumes, though the Dalbergioid clade has similar peptides. They are named nodule-specific cysteine-rich (NCR) peptides due to their exclusive expression in the nodule during symbiosis and the shared 4 or 6 cysteine residue motif. These genes and subsequent proteins vary in number, sequence, and function, but evolutionary genomics research shows that they are adapted from the plant immune system for the new function of symbiont manipulation. In this review, we present the current understanding of NCR peptide biology, expression, and function. We examine NCR genomic and biochemical features and explore their roles in shaping symbiotic outcomes. Finally, we discuss emerging applications and key open questions. Understanding host manipulation of bacterial symbionts within plant tissues provides researchers with targets for engineering more efficient nitrogen-fixing symbioses. In addition, NCR peptides show promise as therapeutic agents with the potential to control both plant and animal pathogens. 

This review presents current knowledge on applying bioelectrochemical sensors to monitor soil fertility through microbial activity and discusses future perspectives. Soil microbial activity is considered an indicator of soil fertility due to the interconnected relationship between soil nutrient composition, microbiome, and plant productivity. Similarities between soils and bioelectrochemical reactors provide the foundation for the design of bioelectrochemical sensors driven by microorganisms enriched as electrochemically active biofilms on polarized electrodes. The biofilm can exchange electrons with electrodes and metabolites with the nearby microbiome to generate electrochemical signals that inform of microbiome functions and nutrient bioavailability. Such mechanisms can be used as a bioelectrochemical sensor for proxy monitoring of soil fertility to address the need for real-time monitoring of soils. 

ABSTRACT Desert kangaroo rats (Dipodomys deserti) construct burrows that can create micro-niches favorable to increased microbial activity. The aim of this study was to characterize the bacterial communities found in kangaroo rat burrows, in proximal desert surface sand, and in samples from kangaroo rats. We collected samples from burrow ceilings of actively inhabited burrows, from burrows that were no longer in use, and from the proximal surface sand in the Sonoran Desert, Yuma, AZ. Following DNA extraction from samples, 16S rRNA gene sequencing was performed, and functional predictions were made and assessed for each characterized bacterial community. Active burrow samples exhibited greater alpha diversity but similar beta diversity when compared to surface sand (P< 0.05), with no significant differences observed between abandoned and active burrows. Bacterial genera and genes related to nitrogen fixation, nitrification, and urea hydrolysis were found in significantly higher abundance in active burrows compared to the surface sand (P< 0.05). The core microbiome of active burrow samples was different from surface sand, including higher abundances ofAcidimicrobialesandAcidobacteriasubdivision Gp7. Active burrow samples included 30 unique genera. Kangaroo rat anal swabs shared 12, cheek pouches shared 6 unique genera with burrows. These findings suggest that kangaroo rats can shape the microbial composition of their burrow environment through the introduction of food material and waste, facilitating increased species richness and bacterial diversity.IMPORTANCEAnimals can alter soil parameters, including microbial composition through burrowing activities, excretion, and dietary composition. Desert kangaroo rats (Dipodomys deserti) construct burrows within loose desert sand that have microclimatic conditions different from the surrounding desert climate. In this study, we explored the effect of disturbance from kangaroo rat activities on the bacterial composition of sand. We compared the bacterial community compositions of kangaroo rat (D. deserti) samples, their burrows, and the proximal surface sand. The results showed that burrow sand shows higher richness and diversity of bacterial community with higher abundances of bacterial genera and genes associated with nitrogen fixation, nitrification, and urea hydrolysis compared to the surface sand. These findings suggest that kangaroo rats affect the microbial composition of their burrow environment through the introduction of food material and waste. 

ABSTRACT Theories explaining the evolution of plant defensive strategies are difficult to experimentally test. Biological invasion scenarios can serve as helpful natural experiments for examining the evolutionary dynamics of plant defenses when plants become established as potential hosts in new environments. This study uses a historical invasion byMedicago polymorpha(Burr Clover) to test the predictive power of the Shifting Defense Hypothesis (SDH) by investigating variation in plant defenses to herbivorous insects. We compared the feeding preferences of a generalist and a specialist herbivore on native and invasive populations ofM. polymorpha. We document a shift in herbivore preference patterns for constitutive versus herbivore‐induced tissues when comparing plants from native and invaded ranges. However, specific biochemical defenses showed a conserved negative correlation between constitutive and inducible defenses across both ranges, indicating a fundamental trade‐off in defense strategy that persists despite allocation differences, suggesting defense evolution that was not revealed by tests in this study. These results provide evidence of evolutionary shifts in plant palatability that are consistent with predictions of the SDH, which predicts evolutionary shifts in defense allocation. Our findings reveal complex evolutionary dynamics that underlie invasion success and demonstrate that invasiveM. polymorphahave undergone evolutionary adaptation in defense strategy beyond any immediate ecological advantages of enemy release, providing insight into how invasive plants successfully adapt to novel herbivore communities over time. 

Microbiota comprise the bulk of life’s diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes symbiotic with plants however, horizontal gene transfer allows for adaptation via gene gain and loss, which could generate fundamentally different evolutionary dynamics. We use comparative genomics and genetics to elucidate the evolutionary mechanisms of adaptation to physiologically stressful serpentine soils in rhizobial bacteria in western North American grasslands. In vitro experiments demonstrate that the presence of a locus of major effect, thenreoperon, is necessary and sufficient to confer adaptation to nickel, a heavy metal enriched to toxic levels in serpentine soil, and a major axis of environmental soil chemistry variation. We find discordance between inferred evolutionary histories of the core genome andnreAXYgenes, which often reside in putative genomic islands. This suggests that the evolutionary history of this adaptive variant is marked by frequent losses, and/or gains via horizontal acquisition across divergent rhizobium clades. However, differentnrealleles confer distinct levels of nickel resistance, suggesting allelic substitution could also play a role in rhizobium adaptation to serpentine soil. These results illustrate that the interplay between evolution via gene gain and loss and evolution via allelic substitution may underlie adaptation in wild soil microbiota. Both processes are important to consider for understanding adaptive diversity in microbes and improving stress-adapted microbial inocula for human use. 

Abstract Background Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs. soil). Results To capture spatial patterns at a regional scale, we sampled the below-ground microbiome of switchgrass monocultures of five sites spanning > 3 degrees of latitude within the Great Lakes region. To capture temporal patterns, we sampled the below-ground microbiome across the growing season within a single site. We compared the strength of spatiotemporal factors to nitrogen addition determining the major drivers in our perennial cropping system. All microbial communities were most strongly structured by sampling site, though collection date also had strong effects; in contrast, nitrogen addition had little to no effect on communities. Though all microbial communities were found to have significant spatiotemporal patterns, sampling site and collection date better explained bacterial than fungal community structure, which appeared more defined by stochastic processes. Root communities, especially bacterial, were more temporally structured than soil communities which were more spatially structured, both across and within sampling sites. Finally, we characterized a core set of taxa in the switchgrass microbiome that persists across space and time. These core taxa represented < 6% of total species richness but > 27% of relative abundance, with potential nitrogen fixing bacteria and fungal mutualists dominating the root community and saprotrophs dominating the soil community. Conclusions Our results highlight the dynamic variability of plant microbiome composition and assembly across space and time, even within a single variety of a plant species. Root and soil fungal community compositions appeared spatiotemporally paired, while root and soil bacterial communities showed a temporal lag in compositional similarity suggesting active recruitment of soil bacteria into the root niche throughout the growing season. A better understanding of the drivers of these differential responses to space and time may improve our ability to predict microbial community structure and function under novel conditions. 

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 before and after a nitrogen fertilization event for established stands on marginal land. We examined community structure and 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 to switchgrass.