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dThis study characterized specific changes in the millet root zone microbiome stimulated by long-term woody-shrub intercropping at different sites in Senegal. At the two study sites, intercropping with woody shrubs and shrub residue resulted in a significant increase in millet [Pennisetum glaucum (L.) R. Br.] yield (P < 0.05) and associated patterns of increased diversity in both bacterial and fungal communities in the root zone of the crop. Across four experiments, operational taxonomic units (OTUs) belonging to Chitinophaga were consistently significantly (P < 0.001) enriched in the intercropped samples, and "Candidatus Koribacter" was consistently significantly enriched in samples where millet was grown alone. Those OTUs belonging to Chitinophaga were enriched more than 30-fold in residue-amended samples and formed a distinct subgroup from all OTUs detected in the genus. Additionally, OTUs belonging to 8 fungal genera (Aspergillus, Coniella, Epicoccum, Fusarium, Gibberella, Lasiodiplodia, Penicillium, and Phoma) were significantly (P < 0.005) enriched in all experiments at all sites in intercropped samples. The OTUs of four genera (Epicoccum, Fusarium, Gibberella, and Haematonectria) were consistently enriched at sites where millet was grown alone. Those enriched OTUs in intercropped samples showed consistently large-magnitude differences, ranging from 30-to 1,000-fold increases in abundance. Consistently enriched OTUs in intercropped samples in the genera Aspergillus, Fusarium, and Penicillium also formed phylogenetically distinct subgroups. These results suggest that the intercropping system used here can influence the recruitment of potentially beneficial microorganisms to the root zone of millet and aid subsistence farmers in producing higher-yielding crops. Subsistence farmers in the Sahel region of sub-Saharan Africa struggle with the challenges of drought, low organic matter in soils, and encroaching desertification (1). Resolving these issues is critical for improving crop yields in this region. Woody shrubs that occur naturally in farmers' fields might be used as part of an intercropping production system to improve crop yields. Two woody shrubs, Guiera senegalensis and Piliostigma reticulatum, are distributed throughout the Sahel region (2, 3). Currently, most farmers manage these shrubs by coppicing, collecting, and burning above-ground residue prior to planting crops. However, agricultural practices in the Sahel region can be adjusted to utilize shrub biomass as a natural source of fertilizer (4). Shrub residue can be added to the soil as a nutrient-rich organic amendment and decompose within an 8-month time period (5). Rhizosphere soils around amended shrubs show increased nutrient content (6), improved soil moisture profiles due to hydraulic lift (7), and a more diverse and complex microfauna soil food web (8). Intercropping with G. senegalensis (9) and P. reticulatum (10), with the incorporation of shrub residue, has also been shown to improve crop yields at two long-term field sites in Senegal...

There is a growing interest by consumers to purchase fresh tomatoes with improved quality traits including lycopene, total soluble solids (TSS), vitamin C, and total titratable acid (TTA) content. As a result, there are considerable efforts by tomato breeders to improve tomato for these traits. However, suitable varieties developed for one location may not perform the same in different locations. This causes a problem for plant breeders because it is too labor-intensive to develop varieties for each specific location. The objective of this study was to determine the extent of genotype · environment (G·E) interaction that influences tomato fruit quality. To achieve this objective, we grew a set of 42 diverse tomato genotypes with different fruit shapes in replicated trials in three locations: North Carolina, New York, and Ohio. Fruits were harvested at the red ripe stage and analyzed for lycopene, TSS, vitamin C, and TTA. Analysis of variance (ANOVA) revealed that there were significant differences (P < 0.05) among tomato genotypes, locations, and their interaction. Further analysis of quality traits from individual locations revealed that there was as much as 211% change in performance of some genotypes in a certain location compared with the average performance of a genotype. Lycopene was found to be most influenced by the environment, whereas TTA was the least influenced. This was in agreement with heritability estimates observed in the study for these quality traits, because heritability estimate for lycopene was 16%, whereas that for TTA was 87%. The extent of G·E interaction found for the fruit quality traits in the tomato varieties included in this study may be useful in identifying optimal locations for future field trials by tomato breeders aiming to improve tomato fruit quality.The cultivated tomato (Solanum lycopersicum L.) is the second most commonly consumed vegetable crop after potato (Solanum tuberosum L.) in the world (FAOSTAT, 2008).

Sea stars are among the most important predators in benthic ecosystems worldwide which is partly attributed to their unique gastrointestinal features and feeding behaviors. Despite their ecological importance, the microbiome of these animals and its influence on adult host health and development largely remains unknown. To begin to understand such interactions we sought to understand what bacteria are associated with these animals, how the microbiome is partitioned across regions of the body and how seawater influences their microbiome. We analyzed the microbiome composition of a geographically and taxonomically diverse set of sea star taxa by using 16S rRNA gene amplicon sequencing and compared microorganisms associated with different regions of their body and to their local environment. In addition, we estimated the bacterial and coelomocyte abundance in the sea star coelomic fluid and bacterioplankton abundance in the surrounding seawater via epifluorescence microscopy. The average bacterial cell abundance observed in the coelomic fluid was one to two orders of magnitude lower than the bacterioplankton abundance in the surrounding seawater suggesting a selection against the presence of microorganisms in the coelomic fluid. The sea star microbiome was also significantly different from seawater with relatively few shared microbial taxa. Microbial communities were found to be significantly different between the pyloric caeca, gonads, coelomic fluid, and body wall of the animals. The most noticeable difference between anatomical sites was the greater relative abundance of Spirochaetae and Tenericutes found in hard tissues (gonads, pyloric caeca, and body wall) than in the coelomic fluid. The microbiome of sea stars thus appears to be anatomically partitioned, distinct from the microbial community of seawater and contains a relatively low abundance of bacteria within the coelomic cavity.

Summary This study coupled a landscape‐scale metagenomic survey of denitrification gene abundance in soils with in situ denitrification measurements to show how environmental factors shape distinct denitrification communities that exhibit varying denitrification activity. Across a hydrologic gradient, the distribution of total denitrification genes (nap/nar + nirK/nirS + cNor/qNor + nosZ) inferred from metagenomic read abundance exhibited no consistent patterns. However, when genes were considered independently, nirS, cNor and nosZ read abundance was positively associated with areas of higher soil moisture, higher nitrate and higher annual denitrification rates, whereas nirK and qNor read abundance was negatively associated with these factors. These results suggest that environmental conditions, in particular soil moisture and nitrate, select for distinct denitrification communities that are characterized by differential abundance of genes encoding apparently functionally redundant proteins. In contrast, taxonomic analysis did not identify notable variability in denitrifying community composition across sites. While the capacity to denitrify was ubiquitous across sites, denitrification genes with higher energetic costs, such as nirS and cNor, appear to confer a selective advantage in microbial communities experiencing more frequent soil saturation and greater nitrate inputs. This study suggests metagenomics can help identify denitrification hotspots that could be protected or enhanced to treat non‐point source nitrogen pollution.

A B S T R A C TAfrican farmers are increasingly adopting sustainable agricultural practices including use of native shrub intercropping approaches. In one village of Sénégal (near Thiès) it was reported that farmers planted mango (Mangifera indica) seedlings within the canopies of a native shrub (Piliostigma reticulatum). Anecdotal information and qualitative observations suggested that the presence of P. reticulatum promoted soil quality and a competitive advantage for establishing mango plantations. We hypothesized that soil chemical and microbial properties of mango rhizosphere soil growing in the presence of P. reticulatum would be significantly improved over soils associated with mango growing outside the influence of P. reticulatum. The results showed that mango-shrub interplanting significantly lowered pH, and increased arbuscular mycorrhizal fungi (AMF) colonization of mango roots, enzyme activities, and microbial biomass compared to mango alone. Phylogenetic analyses by PCR-denaturing gradient gel electrophoresis (DGGE) showed that community structures of fungi, bacteria, and bacterial genes responsible for denitrification (nirK) of the soil from the rooting zone of the mango-shrub intercropping system were distinct from all other soil outside the influence of P. reticulatum. It is concluded that P. reticulatum enhances soil biological functioning and that there is a synergistic effect of intercropping mango with the native shrub, P. reticulatum, in soil quality with a more diverse community, greater AMF infection rates, and greater potential to perform decomposition and mineralize nutrients.

The majority of Earth's humid forests occur on acidic (pH 4.5-5.5) soils (Slessarev et al., 2016;Zhao et al., 2019), with further acidification occurring downwind of industrialized regions driven by anthropogenic acid deposition (e.g. Grenfelt et al., 2020;Vet et al., 2014). Soil pH is one of the strongest predictors of microbial community composition across broad spatial and temporal scales (Bahram et al., 2018;

In many gonochoristic taxa, sex is influenced by developmental environment, a system that can lead to temporal fluctuations in offspring sex ratio. Demographic models suggest that only short-lived species with environmental sex determination (ESD) are negatively impacted by sex-ratio fluctuations, yet these models fail to account for the potential mutation load associated with reductions in genetically effective population sizes. In this study, we developed a series of individual-based simulation models that explore the fixation rates of mildly deleterious alleles under different sexdetermining systems and examine the impacts of variation in lifespan and offspring sex ratio. Populations with ESD exhibited increases in fixation rates in both short-and long-lived populations, but substantial increases were limited to populations characterized by a combination of high sex-ratio variation and short lifespan. Fixation rates were negatively associated with effective population size, indicating that purifying selection operates less efficiently under ESD relative to genotypic sex determination. Reductions in effective population size could be attributed to both intragenerational forces (unequal sex ratio) and intergenerational forces (variable census population sizes). Levels of temporal sex-ratio variation calculated from wild populations of ESD species were capable of yielding large increases in fixation rates, although this relationship was strongly mediated by lifespan. Our results may help to explain the limited phylogenetic distribution of ESD in short-lived taxa.