Structural racism and geographic access to food retailers in the United States: A scoping review.

This scoping review summarized findings and key measures from U.S.-based studies that 1) examined associations between geographic indicators of structural racism (e.g., redlining, racial segregation) and access to food retailers (e.g., supermarkets, convenience stores) or 2) documented disparities in access by neighborhood racial/ethnic composition. In 2022, relevant scientific literature was reviewed using Covidence software. Independent reviewers examined 13,069 citations; 163 citations advanced to the full-text review stage and 70 were selected for inclusion. Twenty-one studies (30%) linked one or more indicator of structural racism to food retailer access while 49 (70%) solely examined differences in access by neighborhood racial/ethnic composition. All studies featuring indicators of structural racism reported significant findings; however, indicators varied across studies making it difficult to make direct comparisons. Key indicators of structural racism in the food access literature included redlining (n = 3), gentrification (n = 3), and racial segregation (n = 4). Many U.S.-based studies have evaluated food retailer access by neighborhood racial/ethnic composition. Moving forward, studies should model indicators of structural racism and determine their influence on geographic access to large and small food retailers.

Genomic features of bacterial adaptation to plants.

Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe-microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering.

Genome-wide identification of bacterial plant colonization genes.

Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizing bacterium, to establish a genome-wide map of bacterial genes required for colonization of the Arabidopsis thaliana root system. We identified 115 genes (2% of all P. simiae genes) with functions that are required for maximal competitive colonization of the root system. Among the genes we identified were some with obvious colonization-related roles in motility and carbon metabolism, as well as 44 other genes that had no or vague functional predictions. Independent validation assays of individual genes confirmed colonization functions for 20 of 22 (91%) cases tested. To further characterize genes identified by our screen, we compared the functional contributions of P. simiae genes to growth in 90 distinct in vitro conditions by RB-TnSeq, highlighting specific metabolic functions associated with root colonization genes. Our analysis of bacterial genes by sequence-driven saturation mutagenesis revealed a genome-wide map of the genetic determinants of plant root colonization and offers a starting point for targeted improvement of the colonization capabilities of plant-beneficial microbes.

Learning Microbial Interaction Networks from Metagenomic Count Data.

Many microbes associate with higher eukaryotes and impact their vitality. To engineer microbiomes for host benefit, we must understand the rules of community assembly and maintenance that, in large part, demand an understanding of the direct interactions among community members. Toward this end, we have developed a Poisson-multivariate normal hierarchical model to learn direct interactions from the count-based output of standard metagenomics sequencing experiments. Our model controls for confounding predictors at the Poisson layer and captures direct taxon-taxon interactions at the multivariate normal layer using an ℓ1 penalized precision matrix. We show in a synthetic experiment that our method handily outperforms state-of-the-art methods such as SparCC and the graphical lasso (glasso). In a real in planta perturbation experiment of a nine-member bacterial community, we show our model, but not SparCC or glasso, correctly resolves a direct interaction structure among three community members that associates with Arabidopsis thaliana roots. We conclude that our method provides a structured, accurate, and distributionally reasonable way of modeling correlated count-based random variables and capturing direct interactions among them.

PLANT MICROBIOME. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa.

Immune systems distinguish "self" from "nonself" to maintain homeostasis and must differentially gate access to allow colonization by potentially beneficial, nonpathogenic microbes. Plant roots grow within extremely diverse soil microbial communities but assemble a taxonomically limited root-associated microbiome. We grew isogenic Arabidopsis thaliana mutants with altered immune systems in a wild soil and also in recolonization experiments with a synthetic bacterial community. We established that biosynthesis of, and signaling dependent on, the foliar defense phytohormone salicylic acid is required to assemble a normal root microbiome. Salicylic acid modulates colonization of the root by specific bacterial families. Thus, plant immune signaling drives selection from the available microbial communities to sculpt the root microbiome.

Isolation and characterization of heparin from tuna skins.

This study characterized heparin isolated from tuna skins. Glycosaminoglycans were isolated from tuna skin after digestion using anion exchange resin. Heparin was eluted from the resin by sodium chloride gradient and was further fractionated by acetone fractionation. Anticoagulant activity was determined using the activated partial thromboplastin time and Heptest assays. Potency was determined using amidolytic antifactor IIa and antifactor Xa assays. The presence of heparin in the extracted tuna skin glycosaminoglycans was confirmed using (13)C-nuclear magnetic resonance. The activated partial thromboplastin time and Heptest clotting times were doubled at concentrations of about 4 and 1 microg/mL, respectively. The clotting time prolongation and antiprotease activity induced by tuna heparin was readily neutralized by 25 microg/mL protamine sulfate. These results demonstrate that biologically active heparin with properties similar to clinical grade heparin can be derived from tuna skin, a raw material with otherwise relatively little economic value.