Ecology

The whiskers of seals are known to function as vibration receptors. Earlier experiments with blindfolded harbour seals in captivity have for example revealed that the animals can detect small water movements, and follow the hydrodynamic trails created by passing objects. But it is unclear if seals in the wild actively use this ability to find prey.
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Widespread occurrence and environmental stimuli responsiveness of trypsin in marine phytoplanktonTo assess whether trypsin occurs broadly in marine phytoplankton and what ecological functions phytoplankton trypsin genes may play, we investigated the occurrence of trypsin genes and environmental stimuli regulating their expression based on PhyloDB, Tara Oceans unigenes and metatranscriptomes datasets. From Tara Oceans unigenes and metatranscriptomes, trypsin homologs were found at all the sampling stations worldwide and in all major phytoplankton phyla (Fig. 1a and Supplementary Fig. 1). The broad phylogenetic representation is corroborated by the prevalence of trypsin in the individual species’ transcriptomes in the PhyloDB database (Fig. 1b), most notably in Bacillariophyta, Dinophyta, Chlorophyta, Cryptophyta and Haptophyta, the major eukaryotic groups of phytoplankton in the ocean. These indicate that trypsin is widely distributed in phytoplankton both taxonomically and geographically, a finding that advances our knowledge on the distribution of this ancient enzyme. Moreover, phylogenetic and structure alignment analysis showed that phytoplankton trypsins are more closely related with bacterial trypsins than metazoan and fungal counterparts, but contain the conserved important residues and structure typical of animal trypsins (Supplementary Figs. 2–4). These observations suggest some complex evolutionary trajectory that might result in functional innovation of phytoplankton trypsin.Fig. 1: Widespread occurrence and environmental nutrient responsiveness of trypsin in global marine phytoplankton.a Wide geographic distribution of trypsin in phytoplankton found in Tara Oceans. Color scale depicts trypsin mRNA abundance. b Wide taxonomic distribution of trypsin in algae found in PhyloDB. c Environmental nutrient drivers of phytoplankton trypsin abundance. Pairwise comparisons of environmental nutrient concentrations are shown with a color gradient denoting Pearson’s correlation coefficient. The trypsin abundance and taxonomic distribution based on the 5–180 µm size fraction from SRF layer from Tara Ocean datasets. Taxonomic trypsin abundance was related to each nutrient factor by partial (geographic distance-corrected) Mantel tests. Edge width corresponds to the Mantel’s r statistic for the corresponding distance correlations, and edge color denotes the statistical significance based on 9999 permutations. Baci Bacillariophyta, Dino Dinophyta, Chlo Chlorophyta, Cryp Cryptophyta, Hapt Haptophyta. Source data are provided as a Source Data file.Full size imageWe found a large amount of trypsin gene duplication, 5 copies to 65 copies in each algal genome we examined6. The evolution of the gene family, in gene sequence and organization relative to other functional domain, need to be treated in a separate paper6, but the rampant gene duplication suggests that trypsin may have important roles in phytoplankton. Moreover, our correlation analysis for trypsin gene expression with environmental parameters in the Tara Oceans metatranscriptomic data showed that the phytoplankton trypsin transcript abundance was correlated with environmental conditions in some taxa, size fractions, and water depths, evidence that trypsin may be important in phytoplankton to adapt to dynamical environmental conditions6. To further explore specific environmental drivers modulating the expression of trypsin, we analyzed distance-corrected dissimilarities of phytoplankton trypsin transcript abundance with environmental nutrient factors using the partial Mantel test. Analyses were restricted to the 5–20 and 20–180 µm size fractions from surface layer as their trypsin appeared to be more responsive to environmental stimuli. As shown in Fig. 1c, trypsin expression in Bacillariophyta, Dinophyta, Chlorophyta, Cryptophyta and Haptophyta was differentially correlated with nutrient availability, most notably in Bacillariophyta and Chlorophyta. Moreover, nitrate and nitrite (NO3, NO3_5m*, and NO3_NO2) and phosphate (PO4) were the strongest correlates of both Bacillariophyta and Chlorophyta trypsin transcript abundances (Fig. 1c). Hence, we posit that trypsin have important functions in the response of phytoplankton to N and P nutrient conditions.Involvement of trypsin in nitrogen and phosphorus nutrient responsesTo gain mechanistic insights into the function of trypsin in phytoplankton, we conducted experiments on the model diatom Phaeodactylum tricornutum. We identified ten trypsin genes from its genome (Supplementary Table 1), and based on qRT-PCR, we observed their growth stage- and condition-specific expression variations (Fig. 2a and Supplementary Fig. 5). Interestingly, one of these genes (PtTryp2) exhibited opposite directions of expression dynamic under N- and P-depleted conditions: downregulated under N-depleted but upregulated under P-depleted condition (Fig. 2a). Furthermore, PtTryp2 transcript increased with increasing cellular N content but decreased with increasing cellular P content (Fig. 2b, c). These results suggest that PtTryp2 is involved in an opposite-direction regulation of responses to nitrogen and phosphorus nutrient status.Fig. 2: Involvement of PtTryp2 in nitrogen and phosphorus nutrient responses.a PtTryp2 expression in P. tricornutum under different growth stages and conditions based on qRT-PCR. Nutrient-replete, HNHP; N-depletion, LNHP; P-depletion, HNLP. Data are presented as mean values ± SD (n = 3 biologically independent samples). The comparisons between the averages of the two groups were evaluated using the one-tailed Student’s t test. The p values with significance (p ≤ 0.05) are shown. b Time-course expression patterns of PtTryp2 when P. tricornutum was grown with different forms of nitrogen nutrients. Data are presented as mean values ± SD (n = 2 biologically independent samples). The comparisons between the averages of the two groups were evaluated using the one-tailed Student’s t test. The p values with significance (p ≤ 0.05) are shown. c PtTryp2 expression pattern after phosphorus supplement. Data are presented as mean values ± SD (n = 3 biologically independent samples). The comparisons between the averages of the two groups were evaluated using the one-tailed Student’s t test. The p values with significance (p ≤ 0.05) are shown. Source data are provided as a Source Data file.Full size imageTo interrogate the function of PtTryp2 in N and P nutrient responses, we analyzed the physiology of homologous overexpression and CRISPR/Cas9 knockout lines we generated. A PtTryp2-overexpression cell line with C-terminal eGFP fusion (named PtTryp2-OE) was generated, and the expression of OE cell line was confirmed at a protein level through Western blot (Fig. 3a). Because the function of a protein corresponds with its subcellular location, we first examined where PtTryp2 is located inside P. tricornutum cells. By computational simulation, we find PtTryp2 is potentially localized in the chloroplast via the secretory pathway (Supplementary Table 2), in accordance with the fact that chloroplasts contain a rather high number of proteases and are the main location of nutrients assimilation and remobilization7. To obtain experimental verification of the chloroplast localization, we carried out subcellular localization analysis in the OE and OEC cell lines using confocal fluorescence microscopy. Interestingly, results show PtTryp2-eGFP are localized in both the chloroplast and cytoplasmic endoplasmic reticulum (ER), to the exclusion of the nucleus and Golgi apparatus, whereas the fluorescence from the eGFP blank vector control is outspread in the cell instead of being co-localized with chloroplast and ER (Fig. 3b and Supplementary Figs. 6–8). Further analyses show that PtTryp2 lacks the C-terminal -(K/H) DEL sequences, a typical ER-retention signal that prevents ER-resident proteins from being transported to downstream locations of the secretory system8,9. Hence, PtTtryp2 is evidently transported via the ER to the chloroplast, as in the case of the previously documented light-harvesting chlorophyll a/b-binding protein in Euglena10.Fig. 3: Subcellular localization of PtTryp2.a Detection of the expression of GFP-PtTryp2 by Western blot using anti-GFP primary antibody. Left panel, GFP-PtTryp2 fusion protein. Middle panel, GFP protein. GAPDH (on the right) was detected using anti-GAPDH as the control to indicate equal protein quantities loaded to each lane. The GFP-PtTryp2 was confirmed expressed successfully at protein level in OE cell line. All experiments were repeated independently three times, and similar results were obtained. b Confocal micrographs showing subcellular localization of GFP-PtTryp2 in chloroplast (PAF, showing red autofluorescence) and endoplasmic reticulum (ER, showing blue fluorescent stain by ER-Tracker) but not in nucleus (Hoechst 33342, showing blue fluorescent stain). TL merge, merger of the fluorescence images with transmission light image. Scale bar, 10 µm, applies to all images. All experiments were repeated independently three times, and similar results were obtained. Source data are provided as a Source Data file.Full size imagePtTryp2 contains one trypsin domain and two internal repeats 1 (RPT) (Fig. 4a), offering one single target for trypsin mutagenesis. Using an optimized efficient CRISPR/Cas9 gene editing system11, we obtained three PtTryp2 mutants with different mutation characteristics in the trypsin domain (named KO1, KO2, and KO3, respectively; Fig. 4b). As shown in Fig. 4c, compared with the knockout control cell line (KOC), all three PtTryp2-KO lines exhibited a significantly diminished PtTryp2 expression under both nutrient depletion and repletion; conversely, the OE cell line displayed markedly elevated PtTryp2 expression in comparison to the overexpression control cell line (OEC). Moreover, the PtTryp2 expression level in KOC cell lines strongly responded to the ambient N and P level, but consistently showed a constant and low expression pattern in KO lines (Fig. 4d). These results verified that KO cell lines with the loss of PtTryp2 function, and OE with enhanced function of PtTryp2, can be used for subsequent functional analyses of PtTryp2.Fig. 4: Mutation generations of PtTryp2 and characters of mutants.a Schematic presentation of PtTryp2 protein. The target site (vertical arrow) for CRISPR/Cas9-based knockout is located within the conserved functional domain (green pentagon), with PAM motif shown in orange font. Red rectangle on the left depicts signal peptide; RPT: internal repeat 1; b Alignment of partial PtTryp2 sequences of the CRISPR/Cas9-generated mutants showing frameshift indels compared to wild type. The frequency by which the sequence was detected within the same colony is indicated in parenthesis. Font color coding: Black, WT sequence; Orange, functional domain containing target for CRISPR/Cas9; Purple, PAM sequence; Blue, Inserted bases; Red dashes, deleted bases. c PtTryp2 expression patterns of knockout and overexpression mutants under different conditions. FC fold change. Data are presented as mean values ± SD (n = 3 biologically independent samples). d PtTryp2 expression of knockout mutants exhibited no response to ambient N and P fluctuation. Data are presented as mean values ± SD (n = 3 biologically independent samples). The comparisons between the averages of the two groups were evaluated using the one-tailed Student’s t test. The p values with significance (p ≤ 0.05) are shown. e Growth curves of different PtTryp2 mutants under different N and P conditions. Nutrient conditions in c–e are indicated by HNHP (Nutrient-replete), LNHP (N-depleted, P-replete), HNLP (N-replete, P-depleted), and LNLP (Nutrient-depleted). Data are presented as mean values ± SD (n = 3 biologically independent samples). Source data are provided as a Source Data file.Full size imageMoreover, we observed the growth physiology of different PtTryp2 mutants across different nutrient conditions. As shown in Fig. 4e and Supplementary Fig. 9, both of the knockout and overexpression of PtTryp2 resulted in decreases in the exponential growth rates (days 1–4) and maximum cell density across different N and P culture conditions. Taken together, these results demonstrate that both elevation and reduction of PtTryp2 expression result in cell growth repression, evidence that PtTryp2 has a crucial role in modulating cell growth in response to different N and P conditions.
PtTryp2 represses nitrogen assimilation and metabolismTranscriptomic data show that PtTryp2 knockout led to the upregulation of most of the nitrogen assimilation and metabolism genes under both N-depleted and replete conditions (Fig. 5a). The transcriptomic data are confirmed to be reproducible based on the correlation analysis of housekeeping genes (Supplementary Fig. 10 and Supplementary Table 3). Notably, the expression fold change of most N assimilation and metabolism genes under N-depleted, P-replete (LNHP) versus nutrient repete (HNHP) conditions were moderated in the PtTryp2 knockout mutant compared to that in its control (KOC), with the exception of GOGAT, which exhibited larger response to the nutrient changes in KOC (Fig. 5a). All these indicate that the inactivation of PtTryp2 enhanced N assimilation and metabolism to mitigate cell stress and reduce overall transcriptomic swing from N-depletion. Under replete conditions (HNHP), substantial transcriptional reprogramming and a significant increase in nitrate uptake rate and cellular N content was observed in the knockout mutants (KO1, KO2 and KO3) (Fig. 5b). The physiological changes were reversed in the overexpression cell lines: a decline in nitrate uptake rate and cellular N content was noted in PtTryp2-OE (Fig. 5c). All the results demonstrate that PtTryp2 functions as a repressor of nitrogen assimilation and metabolism.Fig. 5: Transcriptomic and physiological evidence that PtTryp2 directly represses nitrogen assimilation and metabolism.a PtTryp2 knockout resulted in upregulation of major nitrate-uptake and N-metabolism genes in PtTryp2 knockout (KO1) and control (KOC) under N-depleted (LNHP), P-depleted (HNLP), and nutrient-replete conditions (HNHP). NRT nitrate transporter, NR nitrate reductase, NiR nitrite reductase, GS glutamine synthetase, GOGAT glutamate synthase, GDH glutamate dehydrogenase, 2OG 2-Oxoglutarate; b NO3− uptake rate and cellular N content, increasing dramatically in PtTryp2-KO under HNHP, but decreasing remarkably under HNLP. Data are presented as mean values ± SD (n = 3 biologically independent samples). The comparisons between the averages of the two groups were evaluated using the one-tailed Student’s t test. The p values with significance (p ≤ 0.05) are shown. c NO3− uptake rate and cellular N content, decreasing remarkably in PtTryp2-overexpressing P. tricornutum under HNHP, but increasing under HNLP. Data are presented as mean values ± SD (n = 3 biologically independent samples). The comparisons between the averages of the two groups were evaluated using the one-tailed Student’s t test. The p values with significance (p ≤ 0.05) are shown. d Venn diagram showing the number of N-depletion induced DEGs in PtTryp2-KO1 and KOC. In parentheses, total number of DEGs; red font, upregulated; green font, downregulated. e Log2 fold changes (FC) of N-depletion induced differential gene expression in PtTryp2-KO1 against that in KOC. Most data points (93.37%) are distributed in 1,3 quadrants, indicating the same direction of change. Source data are provided as a Source Data file.Full size imageIn addition, when comparing N-depleted with N-replete conditions, 646 differentially expressed genes (DEGs) were identified in the blank vector control (KOC) but only 187 in PtTryp2-KO1, considerably fewer in the knockout mutant (Fig. 5d). Besides, the magnitude of change was smaller in PtTryp2-KO1 than in KOC for the majority (73%) of the DEGs (Fig. 5e). It is thus evident PtTryp2 in the wild type functions as an amplifier of general metabolic response to N-starvation by repressing nitrogen assimilation and metabolism. Notably, the PtTryp2-KO-promoted and PtTryp2-OE-repressed NO3− uptake patterns observed under nutrient repletion were reversed under P-depletion, indicating that PtTryp2’s roles in N and P signaling are not separated, but rather the protein might mediate the cross-talk between N and P signaling.Besides the direction of action (repression or promotion) shown above, the function of PtTryp2 involves another layer of regulation: the direction of its own expression changes. We find that PtTryp2 expression decreased under N-depletion and increased after N-supplement. Under this two-level regulatory scheme, PtTryp2 is a repressor of N uptake and assimilation genes and a promoter of N starvation-responsiveness in general metabolic pathways per se; yet its own expression decreases under N-limitation to upgrade N-uptake and assimilation under N depletion, and increases under N richness to prevent excessive N-uptake and assimilation; meanwhile, the decreased expression of PtTryp2 actually dampens the dynamic swing in the metabolic landscape in response to N-starvation. This PtTryp2-based regulatory mechanism might enable cells to swiftly respond to fluctuating N availability and cellular demand in order to finetune N responses so that N acquisition is optimized.
PtTryp2 promotes P starvation-induced genes and Pi uptakeAs shown above, PtTryp2 expression is downregulated under N-deficiency to release PtTryp2’s repressing effects on N-starvation response and to promote N uptake, thereby the cells achieve N homeostasis, and an opposite expression pattern of PtTryp2 was observed under P-deficiency, suggesting a N-P coregulation. However, the role of PtTryp2 in P-starvation responses and P homeostasis still needs to be unraveled. Toward that goal, we examined the effects of PtTryp2 inactivation on the expression changes of P starvation-induced genes and the inhibitory regulator of P signaling (SPX), which in plants is a typical P starvation response mechanism12. Consistently, most of Pi transporters (PTs) and alkaline phosphatase (APs) exhibited upregulation to P starvation response in KOC, but most of SPX genes showed downregulation (Fig. 6a).Fig. 6: Transcriptomic and physiological evidence that PtTryp2 positively modulates P starvation-induced genes during Pi starvation.a PtTryp2 knockout resulted in a reverse regulation of most P starvation-induced genes relative to that in control (KOC) under N-depleted (LNHP), P-depleted (HNLP), and nutrient-replete (HNHP) conditions. b PtTryp2 knockout caused decreases in Pi uptake and cellular P content under nutrient-replete condition (HNHP) but caused increases under N-depleted condition (LNHP). Data are presented as mean values ± SD (n = 3 biologically independent samples). The comparisons between the averages of the two groups were evaluated using the one-tailed Student’s t test. The p values with significance (p ≤ 0.05) are shown. c PtTryp2 knockout caused increases in Pi uptake rate and cellular P content under HNHP and LNHP. Data are presented as mean values ± SD (n = 3 biologically independent samples). The comparisons between the averages of the two groups were evaluated using the one-tailed Student’s t test. The p values with significance (p ≤ 0.05) are shown. d Venn diagram showing the number of P-depletion induced DEGs in PtTryp2-KO1 and KOC. In parentheses, total number of DEGs; red font, upregulated; green font, downregulated. e Log2 fold changes (FC) of P-depletion induced differential gene expression in PtTryp2-KO1 against that in KOC. Most data points (95.69%) are distributed in 1,3 quadrants, indicating the same direction of change. Source data are provided as a Source Data file.Full size imageInterestingly, under P-depletion, PtTryp2 knockout downregulated the expression of most of PTs and APs, but upregulated most of the SPX genes (Fig. 6a), revealing PtTryp2’s role in WT to promote P-starvation responses. Consistent with gene transcription, PtTryp2 knockout lowered Pi uptake rate and cellular P content under the nutrient-replete condition (Fig. 6b), whereas an increase was noted in the overexpression cell line PtTryp2-OE (Fig. 6c). Based on RNA-seq, remarkably more DEGs were found for the P-depleted versus nutrient-replete comparison in PtTryp2-KO1 (1501) than that in KOC (277) (Fig. 6d). Besides, in PtTryp2-KO1, the majority of these DEGs (77.25%) exhibited greater fold changes than that in KOC (Fig. 6e). These results indicate that PtTryp2 upregulation in the wild type would dampen metabolic reprogramming in responses to P-limitation, and PtTryp2 downregulation would prevent cells from over P accumulation after P supplement, as opposed to the response to N-depletion. All these findings are indicative that PtTryp2 in the WT functions to upregulate the P starvation-induced genes and restrict general metabolic reconfiguration in response to P-limitation, a mechanism to maintain P homeostasis. Similar to that the PtTryp2-KO-promoted and PtTryp2-OE-repressed NO3− uptake patterns were reversed under P-depletion, the PtTryp2-KO-repressed Pi uptake pattern was reversed under N-depletion (Fig. 6b), implying that PtTryp2 might mediate the cross-talk between N and P signaling. The PtTryp2-OE-promoted Pi uptake pattern was not reversed under N-depletion, however, because N-depletion downregulated the expression of PtTryp2, resulting in the PtTryp2 expression pattern between OEC and OE similar to that under nutrient repletion.
PtTryp2 coordinately regulate N and P uptake and mediates N-P cross-talkGiven the PtTryp2-mediated cross-talk between N and P signaling in P. tricornutum implied in the results presented above, we were tempted to investigate the nature and the mechanism the cross-talk. Here, we uncover Pi and NO3− antagonistic interactions in P. tricornutum, which resemble that in land plants to achieve an optimal N-P nutrient balance13,14. In wild-type (WT) P. tricornutum, we observed a significant repression of NO3− uptake under P starvation and a significant repression of Pi uptake rate under N starvation. Consequently, cellular N content decreased under the P-depleted condition, and cellular P content decreased under the N-depleted condition, relative to nutrient-replete conditions (Fig. 7a, b). In accordance, the transcription of N assimilation and metabolism genes was repressed by P deficiency, and that of P starvation-induced genes was repressed by N limitation (Supplementary Fig. 11). Moreover, transcriptomic results demonstrated that PtTryp2 knockout led to the magnification of Pi and NO3− antagonistic interaction (Supplementary Fig. 11), linking PtTryp2 inactivation to the disruption of the N-P homeostasis. Taken together, our data reveal that PtTryp2’s function operates in opposite directions for N and P responses, but in a coordinated manner, consistent with a role to coregulate N and P signaling.Fig. 7: Illustration that PtTryp2 coordinately regulates N and P acquisition under fluctuating nutritional conditions.a NO3− uptake and cellular N content repressed under HNLP in wild-type cells (WT). Data are presented as mean values ± SD (n = 3 biologically independent samples). The comparisons between the averages of the two groups were evaluated using the one-tailed Student’s t test. The p values with significance (p ≤ 0.05) are shown. b Pi uptake and cellular P content repressed under LNHP in wild-type cells (WT). Data are presented as mean values ± SD (n = 3 biologically independent samples). The comparisons between the averages of the two groups were evaluated using the one-tailed Student’s t test. The p values with significance (p ≤ 0.05) are shown. c Time-course expression of PtTryp2 showed co-varied with the N/P nutrient ratio. Moreover, PtTryp2 expression fluctuated less at the N/P ratio of 16:1 compared to other N/P ratios. The 4 h after nutrient addition represents nutrient-repletion and 72 h nutrient-depletion. Data are presented as mean values ± SD (n = 3 biologically independent samples). d The cellular N/P ratio was significantly elevated by the inactivation of PtTryp2. Data are presented as mean values ± SD (n = 3 biologically independent samples). The comparisons between the averages of the two groups were evaluated using the one-tailed Student’s t test. The p values with significance (p ≤ 0.05) are shown. e The cellular N/P ratio was significantly decreased by the overexpression of PtTryp2. Data are presented as mean values ± SD (n = 3 biologically independent samples). The comparisons between the averages of the two groups were evaluated using the one-tailed Student’s t test. The p values with significance (p ≤ 0.05) are shown. f Hypothetical model depicting the role of PtTryp2 in balancing N and P acquisition. Under N-depletion, PtTryp2 expression is downregulated to promote N-starvation responses and repress P-starvation responses. In contrast, under P-depletion, PtTryp2 expression is upregulated to reinforce P-starvation responses and lessen N-starvation response. By this feedback loop, optimal N-P uptake is achieved to maintain stoichiometric homeostasis. Upregulated genes and enhancement processes are shown in red, downregulated genes and weakened processes colored green. The black arrows depict transcriptional activation. Black bar at line’s end depicts inhibitory regulation. The gray arrows depict possible but unverified interaction between PtTryp2 and the existing P regulating cascade SPX-PHR or an equivalent of the N regulating cascade known in plants (SPX-NLP where NLP stands for NIN-like protein, a transcription factor). Source data are provided as a Source Data file.Full size imageTo further illustrate this, we have carried out PtTryp2 expression pattern analysis across different N/P nutrient stoichiometric ratio conditions, and found that PtTryp2 expression co-varied with the N/P nutrient ratio (Fig. 7c). The time-course analysis showed that PtTryp2 expression fluctuated less under different N or P conditions at the N/P ratio of 16:1 compared to other N/P ratios. The N/P nutrient ratio of 16:1 is considered balanced stoichiometry (Redfield ratio) and appears to be optimal for P. tricornutum growth (Supplementary Fig. 12), as previously documented15, suggesting that at this nutrient stoichiometry there is no need for a significant change in PtTryp2 expression to maintain N/P balance, but other N:P nutrient ratios deviating from 16:1 caused changes in PtTryp2 expression to maintain N/P balance. Moreover, the extent of change in PtTryp2 expression varied between cultures with different levels of N:P nutrient ratios, and between 4 and 72 h after culture inoculation from N- and P-depletion-acclimated parent culture into the experimental nutrient conditions. At 72 h PtTryp2 expression level increased with the degree of P stress (the higher the N:P ratio, the more P stressed the cultures were), except for the N:P = 1:1 condition, an extreme N-limited condition that seemed to cause PtTryp2 expression not to respond according to the general trend. Overall, all these data indicate that PtTryp2 responds strongly to the variability of the N:P ratio. Correspondingly, the cellular N/P ratio under nutrient-repletion also seems to be influenced by PtTryp2 expression level: the cellular N/P ratio was significantly elevated by PtTryp2 knockout, but conversely, was significantly decreased by the overexpression of PtTryp2 (Fig. 7d). Evidently, PtTryp2 serves to coordinate N and P uptake and metabolism to dampen the amplitude of N:P ratio changes that occur when the P. tricornutum cells experience fluctuations in nutrient conditions16,17. That is, PtTryp2 in P. tricornutum acts like an amplitude reducer of the N-P seesaw to achieve the N and P stoichiometric homeostasis (Fig. 7f).As critical nutrients for phytoplankton and plants, the balance and homeostasis of N and P are crucial to the growth of the organisms. For plants, nutrient supply in the soil is highly variable; therefore, to achieve optimal and coordinated utilization of N and P, integration of N and P signaling into an integrated network is required18. Recent studies have revealed the critical components of the network in the model plants Arabidopsis thaliana and Oryza sativa12,19,20,21. Similarly, phytoplankton in the ocean face remarkable environmental nutrient variations, and N and P nutrients are often limited22,23. Although the respective responses to N and P deficiencies have been extensively studied in phytoplankton24,25, an integrative signaling pathway of N-P nutrition cross-talk has remained unknown until now. It is striking to find that trypsin, rather than homologs of plant NRT1.1 and NIGT114,19, mediates and regulates the nitrate-phosphate signaling cross-talk.The two-level model of PtTryp2 function (Fig. 7f), including the direction of PtTryp2 action and the direction of PtTryp2 expression changes, demonstrate that PtTryp2 functions by shifting the setpoints, by tuning its own expression level, at which N signaling or P signaling is triggered in response to environmental nutrient fluctuations so that cells commit to appropriate responses. However, much of the mechanics in the regulatory cascade, from environmental nutrient sensing, PtTryp2-mediated signaling, to the regulation of the effectors such as N- and Pi-transporters and assimilatory genes, remains to be elucidated. Although the interplay between N and P nutrition based on SPX-NLP-NIGT1 and SPX-PHR-NIGT1 cascades, respectively have been uncovered in plants12,19, how PtTryp2 interacts with the SPX-PHR cascade26 and whether a SPX-NLP cascade or other regulatory cascades exist and interact with PtTryp2 for P and N nutrient regulation in phytoplankton remain to be addressed.As an initial attempt, we have performed transcriptional regulatory interaction analysis based on the Inferelator algorithm27 to predict the potential co-regulated genes in the PtTryp2-dependent regulatory cascade. Consequently, a set of 1034 genes co-regulated with PtTryp2 were identified, including 10 transcription factors (Supplementary Table 4), 10 N metabolism and assimilation genes, and a P responsive gene (Supplementary Fig. 13). Moreover, the functional enrichment of the gene set showed that PtTryp2 is possibly involved in post-transcriptional regulation, intracellular signal transduction pathway and kinase-based phosphorus metabolism and recycle pathway (Supplementary Fig. 14). The results hint on a potentially complex regulatory network that requires much more transcriptomes derived from more growth conditions than just the N and P conditions used in this study and other experimental approaches to unravel.We used the potential co-regulated gene list identified in this study in a comparative analysis with the published co-regulatory analysis datasets that contained hundreds of public RNA-seq datasets: DiatomPortal28 and PhaeoNet29. Interestingly, based on the DiatomPortal dataset, the PtTryp2 was found in the Phatr_hclust_0381 hierarchical cluster that consists of 10 genes, which has been identified as the GO term of ubiquitin-dependent protein catabolism. In terrestrial plants, the ubiquitination and degradation of SPX4 was found to mediate the nitrate-phosphate interaction signaling pathway by enabling the release of PHR2 and NLP3 into the nucleus to activate the expression of both phosphate- and nitrate-responsive genes12,19. In addition, we found 120 genes that were common in our gene list and PhaeoNet, some of which are transcription factors.Taken together, our analyses showed that the deletion and overexpression of PtTryp2 simultaneously impacted nitrogen and phosphorus uptake, nitrogen and phosphorus contents of the cell, and the N:P ratio. The simultaneous impact on N and P in opposite directions suggests that this protein either directly regulates the N and P uptake machinery or is close to the direct regulator, e.g., functioning through the ubiquitination and degradation of the direct regulators as in terrestrial plants. Furthermore, it is conceivable that one or more intermediate relays between PtTryp2 and the direct regulator would make it extremely challenging, if not impossible, to exert such precise and coordinated bidirectional regulation on N and P. To understand the mechanics of the regulatory mechanism, co-immunoprecipitation and Chromation immunoprecipitation sequencing are underway in our laboratory to experimentally identify the potential proteins and DNAs interacting with PtTryp2. Further studies on multiple fronts surrounding trypsin and its regulatory pathway are required for gaining an in-depth understanding of the interplay between N and P nutrition in phytoplankton and how phytoplankton will adapt to the potentially more variable and skewed N-P environment in the Anthropocene oceans. More

Dispersal is assumed to contribute to microbiome composition and function; however, it is difficult to measure. Walters et al. now set out a 6-month experiment looking at different dispersal routes of environmental microorganisms to the surface soil layer. They set up different ‘traps’, either glass slides or freshly cut grass, to determine the number, identity and function of incoming microorganisms. The traps ‘recorded’ dispersal through air, from plants and their litter, or from below through the decomposing litter and bulk soil. This was achieved by placing the traps either on a pedestal, closing them off at the bottom or leaving them open, respectively. The authors found that the overall dispersal rate was low, with little influence of the route, with only 0.5% incoming bacterial cells per day compared with the number of resident cells. However, the dispersal routes did influence microbiome composition, at least if from above and close to the surface. Finally, without dispersal, the initial decomposition of the cut grass was slower.
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The Sargasso Sea has long been considered as the spawning area for Atlantic eels, despite the absence of direct observations after more than a hundred years of the survey. We proposed a new insight on the location of Atlantic eels spawning areas eastward of the Sargasso Sea at the intersection between the Mid-Atlantic Ridge and the oceanic fronts1. Our hypothesis is based on a body of corroborating cues from literature. We suggested that European silver eels converge towards the Azores whatever their departure point from Europe and Northern Africa, then they follow the Mid-Atlantic Ridge south westerly until they reach oceanographic fronts where temperature and depths are favourable for reproduction. These orientation behaviours are potentially based on magnetic fields and odours that might be generated by the Mid-Atlantic Ridge volcanic activity and detected by eels during their diel vertical movements. The first favourable meeting point is then located at the crossing between the Mid-Atlantic Ridge and the oceanic thermic isotherms located around 45° W and 26° N. Our hypothesis is supported by (i) microchemical differences between the core of otoliths extracted from leptocephali collected in the Sargasso Sea and from glass eels collected across Europe suggesting that glass eels hatch in different chemical environments than leptocephali (ii) an asymmetric genetic introgression between American and European eels2 suggesting that the overlapping spawning areas favour transport of hybrids towards northern Europe rather than to America and to southern Europe. This supports the possible existence of several distinct spawning areas, where currents favour transport either westward (American eel), north eastward (hybrids and European eels) or eastward (European eels). To test this hypothesis, we developed a transport model and compared the dispersion dynamics of virtual leptocephali released from the Sargasso Sea and from above the Mid-Atlantic Ridge. The transport models showed that virtual eels released from the Mid-Atlantic Ridge reached Europe and America following similar patterns than those released from the Sargasso Sea thus supporting the Mid-Atlantic Ridge spawning hypothesis.Hanel et al.3 have raised several concerns, one of which being that “microchemical evidence was the only was the major argument supporting the Mid-Atlantic Ridge hypothesis”. This was their start point of a critical rebuttal of our findings to question our hypothesis. Instead, we consider that our regrettable error does not fundamentally contradict the possibility that eels do indeed successfully spawn outside the so-called Sargasso Sea.(Comment 1) The importance of seamounts as orientation and navigation cues towards a spawning area was hypothesized, no clear mechanism is proposed for how the migrating eels can detect the ridge.(Response 1) Our Hypothesis does not state that eels find a kind of shallow seamount where they spawn. Instead, we propose that orientation of silver eels during their spawning migration could be based on a combination of behavioural mechanisms including geomagnetism, odours, temperature and salinity gradients4,5,6,7,8. These environmental cues and related gradients are strongly controlled or influenced by the topography of the oceanic floor. The Mid-Atlantic Ridge and the Mariana areas have similarities with ridges and seamount chains oriented perpendicularly to temperature and salinity fronts surrounded by deep abyssal plains. Our Mid-Atlantic Ridge hypothesis proposed that Atlantic eels could use similar signposts as Japanese eel, which hatch near the Mariana Ridge9. Indeed, as for the Japanese eels, the orientation mechanism that lead Atlantic eels from the growth areas to the ridge are not understood, but the empirical observations from Righton et al.10 suggest that eels converge towards the Azores whatever their release point across Europe and that their diel vertical migration takes them down to 500–1000 m every day. The reasons for this behaviour are not elucidated, but since they cost energy, they are likely compensated by advantages such as orientation together with predator avoidance and sexual maturation11,12,13. Following our hypothesis, eels search for orientation cues during DVM. The geomagnetic fields are suggested to provide detectable information for silver eels on their oceanic spawning migration14. However, whether magnetic characteristics of the Mid-Atlantic ridge may provide detectable orientation cues still needs to be documented. Similarly, the existence of detectable odours that might be generated by the tectonic activity and hydrodynamics of the Mid-Atlantic ridge and serve as orientation cues for eels is still unknown. Hydrodynamic mesoscale turbulence and vertical flows have been shown to be generated along the Mid-Atlantic Ridge15, which we propose eels might be able to detect. There are no well supported spawning areas of freshwater eels other than A. japonica and one north Pacific population of A. marmorata. The spawning areas of the other species remain unknown. In the south west Indian Ocean, spawning areas of 3 species (A. mossambica, A. marmorata and A. bicolor) were proposed on the east of the Mascarene Ridge with a similar topography (although shallower) than along the Mid-Atlantic Ridge and the Mid-Pacific ridge and seamounts16,17. Inaccurate spawning areas were also proposed for the South Pacific A. diffenbachii between Fiji, New Caledonia and New Zealand; in the vicinity of a number of oceanic ridges and trenches18 that may also serve as landmarks. Because all eel species studied on their spawning migration show similar diel vertical migration behaviours, it is likely that common orientation mechanisms could lead to detection of oceanographic variability related to the topography of the sea floor and related geomagnetism, local hydrodynamic turbulence and odour caused by vertical currents. This kind of oceanic landscape (chains of seamounts) occurs on narrow areas which strongly increase the meeting probability of spawners searching for partners and favourable spawning places.(Comment 2) Drift simulation with departures from the Mid-Atlantic Ridge and from the Sargasso Sea showed similar results. This is not surprising since the modelling of larval drift seems essentially just to reflect the slow westward drift prevailing both in the Sargasso Sea and Mid-Atlantic Ridge areas. The assumption of using the intersection of the Mid-Atlantic Ridge by the two thermal fronts as presumed spawning places seems to have little basis. There is no indication neither of one nor two temperature fronts at depths where leptocephali are found along a 45  W latitudinal section in the middle of the Mid-Atlantic Ridge area.(Response 2) We agree with the comments that the similar distributions between the departure from the Sargasso Sea and the Mid-Atlantic Ridge are expected, as they mainly reflect the ocean circulation. This is also what we wanted to address, if different departures could lead to similar distributions, either Sargasso Sea or Mid-Atlantic Ridge could be candidates for the spawning area. We also agree that many eel larvae were collected at the two fronts in the Sargasso Sea, but not near the Mid-Atlantic Ridge. However, if the departure from the Sargasso Sea and the Mid-Atlantic Ridge led to similar distributions after 720 days, they were not the result of westward current, but the cause of a relatively quiet ocean in the Sargasso Sea and its surrounding area (i.e. Fig. 1). Without prevailing current, small larvae were mainly transported by ocean dispersion, and would later be transported by the major currents that lie in the north (Azores Current), south (North Equatorial Current), and west (Gulf Stream) of the Sargasso Sea. So, we compared departures at 100 km from west and east of the Mid-Atlantic Ridge. Subtle differences occurred (figure below). V-larvae departing from the east of the ridge dispersed relatively less northward compared to larvae released 100 km at the west of the ridge (this figure and original paper). Secondly v-larvae released at the south east of the study area (red dots on the figure, right panel) disperse relatively less towards the Caribbean Sea than when released at the west (red dots of the figure, left panel). This suggests that the dispersion of European eel larvae is optimum in an area comprised between the Mid-Atlantic Ridge and the Sargasso Sea (our previous simulation in the original paper), and declines eastward of the Mid-Atlantic Ridge (present simulation below).Figure 1Distribution of v-larvae released departure at the west (left) and east (right) of Mid-Atlantic Ridge. The tracking method is the same as described in the paper, v-larvae were release within 100 km west and east of the ridge.Full size imageHanel et al. also indicate that the convergence front weakens from West, in the Sargasso Sea, to East above the ridge. We consider that this constitutes an additional argument that the Mid-Atlantic Ridge is indeed at the edge of the convergence zone at the first area of the Atlantic Ocean where currents and temperatures are favourable for reproduction of eels.(Comment 3) Elevated manganese (Mn) concentrations in the otolith cores of glass eels as a hint for successful spawning only in areas with volcanic activity based on observations of Martin et al.18. However, the results from Martin et al.19 were entirely misread, resulting in a mis-interpretation of the data.(Response 3) Based on Martin et al.19, we stated that higher concentrations of Mn were found in glass eels’ otoliths collected across European estuaries than in otoliths of leptocephali larvae sampled in the Sargasso Sea. We suggested that this was the indication that glass eels were born in areas where volcanic activity produces high loads of Mn and other metals. This formed one of the arguments supporting our hypothesis that Atlantic eels could spawn in the proximity to the Mid-Atlantic Ridge. Thanks to Reinhold Hanel and colleagues, we realized that Martin et al.19 in fact showed that concentrations of Mn were higher in the center of otoliths of leptocephali larvae than in those of glass eels collected along the European coasts. Consequently, this argument is no longer valid. Nonetheless, otolith microchemical fingerprints significantly differ between young leptocephali sampled in the Sargasso Sea in 2008 and glass eels collected in Europe, hence suggesting that they have distinct spawning areas19. These authors indicated that the incorporation of elements from the environment to the otoliths needed to be better understood, namely as stated by Hanel et al., because of physiological and environmental control such as temperature and salinity. In addition, they outline that the dynamics of elements from the sea floor to the subsurface is not well understood and could be slow. We totally share these conclusions that are well known facts, and that simply confirm that environmental characteristics (trace element concentrations, salinity and temperature) are responsible for the elemental signature of the central part of otoliths. Hanel et al. also state that the composition of otoliths are also controlled by elemental maternal transfer from the egg to the otoliths. We are aware of this fact that has been shown is other fish species. However, the laser ablations were performed after the first feed check where maternal influence is reduced and is overruled by environment18. This supports the idea that glass eels collected in Europe do not originate from the same environments as leptocephali captured in the Sargasso Sea.(Comment 4) Insufficient sampling efforts and a limited area coverage of recent surveys as a possible reason for “false negative” observations along the Mid-Atlantic Ridge. This statement does not recognize the investigations by Johannes Schmidt as well as earlier and later surveys in the Mid-Atlantic Ridge area. The ICES “Eggs and Larvae database” records a total of 48 A anguilla leptocephali caught within the area 15–29 N and 43–48 W, at 10 stations between 1913 and 1970.Thanks for pointing out that larvae have been caught near the Mid-Atlantic Ridge, in which larvae were not newly hatched because of their relatively large size (23–45 mm). Ocean currents were weak and could flow either eastward or westward in this region, indicating that the spawning could occur from west to east of the ridge, without considering swimming. Note that ocean currents could change directions, so that it was also possible to spawn near the ridge after been transported eastward and westward.The observed distribution of small larvae  More

Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, DenmarkMorten Kam Dahl Dueholm, Marta Nierychlo, Kasper Skytte Andersen, Vibeke Rudkjøbing, Simon Knutsson, Per H. Nielsen, Mads Albertsen & Per Halkjær NielsenEnvironmental Science Department, The Institute for Scientific and Technological Research of San Luis Potosi (IPICYT), San Luis Potosí, MexicoSonia ArriagaDepartment of Process, Energy and Environmental Technology, University College of Southeast Norway, Porsgrunn, NorwayRune BakkeCenter for Microbial Ecology and Technology, Ghent University, Ghent, BelgiumNico BoonInstitute for Water and Wastewater Technology, Durban University of Technology, Durban, South AfricaFaizal Bux & Sheena KumariVeolia Water Technologies AB, AnoxKaldnes, Lund, SwedenMagnus ChristenssonDepartment Of Chemical Engineering, Faculty of Engineering, University of Malaya, Kuala Lumpur, MalaysiaAdeline Seak May ChuaEnvironmental Engineering, Newcastle University, Newcastle, EnglandThomas P. CurtisThe Cytryn Lab, Microbial Agroecology, Volcani Center, Agricultural Research Organization, Rishon Lezion, IsraelEddie CytrynINGEBI-CONICET, University of Buenos Aires, Buenos Aires, ArgentinaLeonardo ErijmanDepartment of Biochemistry and Microbial Genetics, Biological Research Institute “Clemente Estable”, Montevideo, UruguayClaudia EtchebehereNIREAS-International Water Research Center, University of Cyprus, Nicosia, CyprusDespo Fatta-KassinosEnvironmental Engineering, McGill University, Montreal, QC, CanadaDominic FrigonSchool of Microbiology, Universidad de Antioquia, Medellín, ColombiaMaria Carolina Garcia-ChavesSchool of Civil and Environmental Engineering, Cornell University, Ithaca, NY, USAApril Z. GuWater Chemistry and Water Technology and DVGW Research Laboratories, Karlsruhe Institute of Technology (KIT), Karlsruhe, GermanyHarald HornDavid Jenkins & Associates, Inc, Kensington, CA, USADavid JenkinsInstitute for Water Quality and Resource Management, TU Wien, Vienna, AustriaNorbert KreuzingerWater Innovation and Research Centre, University of Bath, Bath, EnglandAna LanhamSingapore Centre of Environmental Life Sciences Engineering (SCELSE) Nanyang Technological University, Singapore, SingaporeYingyu LawWater Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi ArabiaTorOve LeiknesProcess Engineering in Urban Water Management, ETH Zürich, Zürich, SwitzerlandEberhard MorgenrothDepartment of Biology, Warsaw University of Technology, Warsaw, PolandAdam MuszyńskiEnvironmental Microbial Genetics Lab, La Trobe University, Melbourne, VIC, AustraliaSteve PetrovskiTechnologies and Evaluation Area, Catalan Institute for Water Research, ICRA, Girona, SpainMaite PijuanVA Tech Wabag Ltd, Chennai, IndiaSuraj Babu PillaiBiochemical Engineering Group, Universidade Nova de Lisboa, Lisboa, PortugalMaria A. M. ReisState Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, ChinaQi RongWater Research Institute IRSA – National Research Council (CNR), Rome, ItalySimona RossettiLa Trobe University, Melbourne, VIC, AustraliaRobert SeviourDepartment of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, MA, USANick TookerKemira Oyj, Espoo R&D Center, Espo, FinlandPirjo VainioEnvironmental Biotechnology, TU Delft, Delft, The NetherlandsMark van LoosdrechtVA Tech Wabag, Philippines Inc., Makati City, PhilippinesR. VikramanDepartment of Water Technology and Environmental Engineering, University of Chemistry and Technology, Prague, Czech RepublicJiří WannerEnvironmental Life Science Engineering, TU Delft, Delft, The NetherlandsDavid WeissbrodtSchool of Environment, Tsinghua University, Beijing, ChinaXianghua WenEnvironmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, Hong KongTong Zhang More