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We conducted feeding experiments with sardine (Sardinops melanostictus) and Japanese flounder (Paralichthys olivaceus) to investigate trophic discrimination factors (TDFs) in bone collagen using retrospective isotope analysis. Sardines and Japanese flounder were fed a single diet for 9 months and 4 months, respectively. At the end of the experiments, we extracted vertebral centra from six sardines and seven Japanese flounder and subdivided them into multiple sections. We extracted bone collagen from each section, and measured the δ13C and δ15N of each vertebral section and food source. In all fish samples, the δ13C and δ15N values of bone collagen increased from the centers of vertebrae to the marginal sections. This trend was consistent with the predicted isotopic shift in the diets of these fishes. The TDFs for sardines were estimated at 5.58 ± 0.25‰ (mean ± SD) for δ13C and −0.70 ± 0.25‰ for δ15N; those for Japanese flounder were 3.89 ± 0.14‰ for δ13C and 1.18 ± 0.35‰ for δ15N. Our results show that segmental analysis of vertebrae can reconstruct δ13C and δ15N values for multiple life‐stages of both fish species and is useful for estimating TDFs and turnover times of fish bone collagen.

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Plants usually promote pollutant bioremediation by several mechanisms including modifying the diversity of functional microbial species. However, conflicting results are reported that root exudates have no effects or negative effects on organic pollutant degradation. In this study, we investigated the roles of ryegrass in phenanthrene degradation in soils using DNA stable isotope probing (SIP) and metagenomics to reveal a potential explanation for conflicting results among phytoremediation studies. Phenanthrene biodegradation efficiency was improved by 8% after 14 days of cultivation. Twelve and ten operational taxonomic units (OTUs) were identified as active phenanthrene degraders in non-rhizosphere and rhizosphere soils, respectively. The active phenanthrene degraders exhibited higher average phylogenetic distances in rhizosphere soils (0.33) than non-rhizosphere soils (0.26). The K a/K s values (the ratio of nonsynonymous to synonymous substitutions) were about 10.37% higher in the rhizosphere treatment among >90% of all key carbohydrate metabolism-related genes, implying that ryegrass may be an important driver of microbial community variation in the rhizosphere by relieving the carbohydrate metabolism pressure and improving the survival ability of r-strategy microbes. Most K a/K s values of root-exudate-related metabolism genes exhibited little change, except for fumarate hydratase that increased 13-fold in the rhizosphere compared to that in the non-rhizosphere treatment. The K a/K s values of less than 50% phenanthrene-degradation-related genes were affected, 30% of which increased and 70% behaved oppositely. Genes with altered K a/K s values had a low percentage and followed an inconsistent changing tendency, indicating that phenanthrene and its metabolites are not major factors influencing the active degraders. These results suggested the importance of carbohydrate metabolism, especially fumaric acid, in rhizosphere community shift, and hinted at a new hypothesis that the rhizosphere effect on phenanthrene degradation efficiency depends on the existence of active degraders that have competitive advantages in carbohydrate and fumaric acid metabolism.