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The rhizosphere constitutes a dynamic interface between plant hosts and their associated microbial communities. Despite the acknowledged potential for enhancing plant fitness by manipulating the rhizosphere, the engineering of the rhizosphere microbiome through inoculation has posed significant challenges. These challenges are thought to arise from the competitive microbial ecosystem where introduced microbes must survive, and the absence of adaptation to the specific metabolic and environmental demands of the rhizosphere. Here, we engineered a synthetic rhizosphere community (SRC1) with the anticipation that it would exhibit a selective advantage in colonizing the host Sorghum bicolor, thereby potentially fostering its growth. SRC1 was assembled from bacterial isolates identified either for their potential role in community cohesion through network analysis or for their ability to benefit from host-specific exudate compounds. The growth performance of SRC1 was assessed in vitro on solid media, in planta under gnotobiotic laboratory conditions, and in the field. Our findings reveal that SRC1 cohesion is most robust when cultivated in the presence of the plant host under laboratory conditions, with lineages being lost from the community when grown either in vitro or in a native field setting. We establish that SRC1 effectively promotes the growth of both above- and below-ground plant phenotypes in both laboratory and native field contexts. Furthermore, in laboratory conditions, these growth enhancements correlate with the transcriptional dampening of lignin biosynthesis in the host. Collectively, these results underscore the potential utility of synthetic microbial communities for modulating crop performance in controlled and native environments alike.

A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production.

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.

Per- and polyfluoroalkyl substances (PFAS) are a widespread and persistent class of contaminants posing significant environmental and human health concerns. Comprehensive understanding of the modes of action underlying toxicity among structurally diverse PFAS is mostly lacking. To address this need, we recently reported on our application of developing zebrafish to evaluate a large library of PFAS for developmental toxicity. In the present study, we prioritized 15 bioactive PFAS that induced significant morphological effects and performed RNAsequencing to characterize early transcriptional responses at a single timepoint (48 h post fertilization) after early developmental exposures (8 h post fertilization). Internal concentrations of 5 of the 15 PFAS were measured from pooled whole fish samples across multiple timepoints between 24-120 h post fertilization, and additional temporal transcriptomics at several timepoints (48-96 h post fertilization) were conducted for Nafion byproduct 2. A broad range of differentially expressed gene counts were identified across the PFAS exposures. Most PFAS that elicited robust transcriptomic changes affected biological processes of the brain and nervous system development. While PFAS disrupted unique processes, we also found that similarities in some functional head groups of PFAS were associated with the disruption in expression of similar gene sets. Body burdens after early developmental exposures to select sulfonic acid PFAS, including Nafion byproduct 2, increased from the 24-96 h post fertilization sampling timepoints and were greater than those of sulfonamide PFAS of similar chain lengths. In parallel, the Nafion byproduct 2-induced transcriptional responses increased between 48 and 96 h post fertilization. PFAS characteristics based on toxicity, transcriptomic effects, and modes of action will contribute to further prioritization of PFAS structures for testing and informed hazard assessment. [ABSTRACT FROM AUTHOR]

This article explores the occurrence of algal blooms in nutrient-poor lakes, particularly in high-elevation mountain lakes. The authors propose that warming-induced changes in redox conditions may be a common factor in these blooms. Climate change-related warming reduces oxygen levels and enhances microbial processes, leading to the release of nutrients that can be utilized by benthic algae. The article also acknowledges that other factors, such as nutrient loading and changes in the food web, can contribute to these blooms. The authors call for further research to test their hypothesis. Additionally, the article discusses the role of oxygen availability and temperature fluctuations in promoting the growth of periphyton blooms in the littoral zones of lakes. The fluctuations in oxygen and temperature create favorable conditions for nutrient release from sediments, which are then intercepted by periphyton. The article highlights the need for more research on temperature and oxygen dynamics, nutrient flux, and microbial dynamics in lake sediments. [Extracted from the article]