Ecology

Stocker, T. F. et al. Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (eds T.F. Stocker et al.) Ch. TS, 33–115 (Cambridge University Press, 2013).Doney, S. C., Fabry, V. J., Feely, R. A. & Kleypas, J. A. Ocean acidification: The other CO2 problem. Ann. Rev. Mar. Sci. 1, 169–192 (2009).PubMed 
Article 

Google Scholar 
Albright, R. et al. Carbon dioxide addition to coral reef waters suppresses net community calcification. Nature 555, 516–519 (2018).ADS 
PubMed 
Article 

Google Scholar 
Chen, C.-T.A. et al. Deep oceans may acidify faster than anticipated due to global warming. Nat. Clim. Chang. 7, 890–894 (2017).ADS 
Article 

Google Scholar 
Guinotte, J. M. et al. Will human-induced changes in seawater chemistry alter the distribution of deep-sea scleractinian corals?. Front. Ecol. Environ. 4, 141–146 (2006).Article 

Google Scholar 
Figuerola, B. et al. A review and meta-analysis of potential impacts of ocean acidification on marine calcifiers from the southern ocean. Front. Mar. Sci. 8, 584445 (2021).Article 

Google Scholar 
Ries, J. B. Skeletal mineralogy in a high-CO2 world. J. Exp. Mar. Biol. Ecol. 403, 54–64 (2011).Article 

Google Scholar 
Blackmon, P. D. & Todd, R. Mineralogy of some foraminifera as related to their classification and ecology. J. Paleontol. 33, 1–15 (1959).
Google Scholar 
Oliver, W. A. Jr. The relationship of the scleractinian corals to the rugose corals. Paleobiology 6, 146–160 (1980).Article 

Google Scholar 
Sinclair, D. J. et al. Reproducibility of trace element profiles in a specimen of the deep-water bamboo coral Keratoisis sp. Geochim. Cosmochim. Acta 75, 5101–5121 (2011).ADS 
Article 

Google Scholar 
Liu, Y.-W., Sutton, J. N., Ries, J. B. & Eagle, R. A. Regulation of calcification site pH is a polyphyletic but not always governing response to ocean acidification. Sci. Adv. 6, eaax1314 (2020).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Cornwall, C. E. et al. Understanding coralline algal responses to ocean acidification: Meta-analysis and synthesis. Glob. Change Biol. 28, 362–374 (2022).Article 

Google Scholar 
Al-Horani, F. A., Al-Moghrabi, S. M. & de Beer, D. Microsensor study of photosynthesis and calcification in the scleractinian coral, Galaxea fascicularis: Active internal carbon cycle. J. Exp. Mar. Biol. Ecol. 288, 1–15 (2003).Article 

Google Scholar 
Al-Horani, F. A., Al-Moghrabi, S. M. & de Beer, D. The mechanism of calcification and its relation to photosynthesis and respiration in the scleractinian coral Galaxea fascicularis. Mar. Biol. 142, 419–426 (2003).Article 

Google Scholar 
Le Goff, C. et al. In vivo pH measurement at the site of calcification in an octocoral. Sci. Rep. 7, 11210 (2017).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
McCulloch, M. et al. Resilience of cold-water scleractinian corals to ocean acidification: Boron isotopic systematics of pH and saturation state up-regulation. Geochim. Cosmochim. Acta 87, 21–34 (2012).ADS 
Article 

Google Scholar 
Gilbert, P. U. P. A. et al. Biomineralization: Integrating mechanism and evolutionary history. Sci. Adv. 8, eabl9653 (2022).PubMed 
PubMed Central 
Article 

Google Scholar 
Donald, H. K., Ries, J. B., Stewart, J. A., Fowell, S. E. & Foster, G. L. Boron isotope sensitivity to seawater pH change in a species of Neogoniolithon coralline red alga. Geochim. Cosmochim. Acta 217, 240–253 (2017).ADS 
Article 

Google Scholar 
Krief, S. et al. Physiological and isotopic responses of scleractinian corals to ocean acidification. Geochim. Cosmochim. Acta 74, 4988–5001 (2010).ADS 
Article 

Google Scholar 
Hönisch, B. et al. Assessing scleractinian corals as recorders for paleo-pH: Empirical calibration and vital effects. Geochim. Cosmochim. Acta 68, 3675–3685 (2004).ADS 
Article 

Google Scholar 
Anagnostou, E., Williams, B., Westfield, I., Foster, G. L. & Ries, J. B. Calibration of the pH-δ11B and temperature-Mg/Li proxies in the long-lived high-latitude crustose coralline red alga Clathromorphum compactum via controlled laboratory experiments. Geochim. Cosmochim. Acta 254, 142–155 (2019).ADS 
Article 

Google Scholar 
Cornwall, C. E., Comeau, S. & McCulloch, M. T. Coralline algae elevate pH at the site of calcification under ocean acidification. Glob. Change Biol. 23, 4245–4256 (2017).ADS 
Article 

Google Scholar 
Rosenthal, Y., Lear, C. H., Oppo, D. W. & Linsley, B. K. Temperature and carbonate ion effects on Mg/Ca and Sr/Ca ratios in benthic foraminifera: Aragonitic species Hoeglundina elegans. Paleoceanography 21, PA1007 (2006).ADS 
Article 

Google Scholar 
Gori, A. et al. Physiological response of the cold-water coral Desmophyllum dianthus to thermal stress and ocean acidification. PeerJ 4, e1606 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Gagnon, A. C., Gothmann, A. M., Branson, O., Rae, J. W. B. & Stewart, J. A. Controls on boron isotopes in a cold-water coral and the cost of resilience to ocean acidification. Earth Planet. Sci. Lett. 554, 116662 (2021).Article 

Google Scholar 
Cairns, S. D. Global diversity of the Stylasteridae (Cnidaria: Hydrozoa: Athecatae). PLoS ONE 6, e21670 (2011).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Cairns, S. D. Deep-water corals: An overview with special reference to diversity and distribution of deep-water scleractinian corals. Bull. Mar. Sci. 81, 311–322 (2007).
Google Scholar 
Samperiz, A. et al. Stylasterid corals: A new paleotemperature archive. Earth Planet. Sci. Lett. 545, 116407 (2020).Article 

Google Scholar 
Cairns, S. D. & Macintyre, I. G. Phylogenetic implications of calcium carbonate mineralogy in the Stylasteridae (Cnidaria: Hydrozoa). Palaios, 96–107 (1992).Anagnostou, E., Huang, K. F., You, C. F., Sikes, E. L. & Sherrell, R. M. Evaluation of boron isotope ratio as a pH proxy in the deep sea coral Desmophyllum dianthus: Evidence of physiological pH adjustment. Earth Planet. Sci. Lett. 349–350, 251–260 (2012).ADS 
Article 

Google Scholar 
Rae, J. W. B. et al. CO2 storage and release in the deep Southern Ocean on millennial to centennial timescales. Nature 562, 569–573 (2018).ADS 
PubMed 
Article 

Google Scholar 
Farmer, J. R., Hönisch, B., Robinson, L. F. & Hill, T. M. Effects of seawater-pH and biomineralization on the boron isotopic composition of deep-sea bamboo corals. Geochim. Cosmochim. Acta 155, 86–106 (2015).ADS 
Article 

Google Scholar 
Sutton, J. N. et al. δ11B as monitor of calcification site pH in divergent marine calcifying organisms. Biogeosciences 15, 1447–1467 (2018).ADS 
Article 

Google Scholar 
Heinemann, A. et al. Conditions of Mytilus edulis extracellular body fluids and shell composition in a pH-treatment experiment: Acid-base status, trace elements and δ11B. Geochem. Geophys. Geosyst. 13, 1–17 (2012).Article 

Google Scholar 
Rae, J. W. B., Foster, G. L., Schmidt, D. N. & Elliott, T. Boron isotopes and B/Ca in benthic foraminifera: Proxies for the deep ocean carbonate system. Earth Planet. Sci. Lett. 302, 403–413 (2011).ADS 
Article 

Google Scholar 
Auscavitch, S. R. et al. Distribution of deep-water scleractinian and stylasterid corals across abiotic environmental gradients on three seamounts in the Anegada Passage. PeerJ 8, e9523 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
DeCarlo, T. M., Holcomb, M. & McCulloch, M. T. Reviews and syntheses: Revisiting the boron systematics of aragonite and their application to coral calcification. Biogeosciences 15, 2819–2834 (2018).ADS 
Article 

Google Scholar 
McCulloch, M. T., D’Olivo, J. P., Falter, J., Holcomb, M. & Trotter, J. A. Coral calcification in a changing world and the interactive dynamics of pH and DIC upregulation. Nat. Commun. 8, 15686 (2017).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Henehan, M. J. et al. Calibration of the boron isotope proxy in the planktonic foraminifera Globigerinoides ruber for use in palaeo-CO2 reconstruction. Earth Planet. Sci. Lett. 364, 111–122 (2013).ADS 
Article 

Google Scholar 
Rink, S., Kühl, M., Bijma, J. & Spero, H. Microsensor studies of photosynthesis and respiration in the symbiotic foraminifer Orbulina universa. Mar. Biol. 131, 583–595 (1998).Article 

Google Scholar 
Fietzke, J. & Wall, M. Distinct fine-scale variations in calcification control revealed by high-resolution 2D boron laser images in the cold-water coral Lophelia pertusa. Sci. Adv. 8, eabj4172 (2022).PubMed 
PubMed Central 

Google Scholar 
Drake, J. L. et al. How corals made rocks through the ages. Glob. Change Biol. 26, 31–53 (2020).ADS 
Article 

Google Scholar 
Blamart, D. et al. Correlation of boron isotopic composition with ultrastructure in the deep-sea coral Lophelia pertusa: Implications for biomineralization and paleo-pH. Geochem. Geophys. Geosyst. 8, Q12001 (2007).ADS 
Article 

Google Scholar 
Jurikova, H. et al. Boron isotope composition of the cold-water coral Lophelia pertusa along the Norwegian margin: Zooming into a potential pH-proxy by combining bulk and high-resolution approaches. Chem. Geol. 513, 143–152 (2019).ADS 
Article 

Google Scholar 
NOAA Deep Sea Coral Research & Technology Program. NOAA National Database for Deep-Sea Corals and Sponges (version 20201021-0), https://deepseacoraldata.noaa.gov/ (2017).Dickson, A. G. Thermodynamics of the dissociation of boric acid in synthetic seawater from 273.15 to 318.15 K. Deep Sea Res. Part A Oceanogr. Res. Pap. 37, 755–766 (1990).ADS 
Article 

Google Scholar 
Stewart, J. A., Anagnostou, E. & Foster, G. L. An improved boron isotope pH proxy calibration for the deep-sea coral Desmophyllum dianthus through sub-sampling of fibrous aragonite. Chem. Geol. 447, 148–160 (2016).ADS 
Article 

Google Scholar 
Mavromatis, V., Montouillout, V., Noireaux, J., Gaillardet, J. & Schott, J. Characterization of boron incorporation and speciation in calcite and aragonite from co-precipitation experiments under controlled pH, temperature and precipitation rate. Geochim. Cosmochim. Acta 150, 299–313 (2015).ADS 
Article 

Google Scholar 
Holcomb, M., DeCarlo, T. M., Gaetani, G. A. & McCulloch, M. Factors affecting B/Ca ratios in synthetic aragonite. Chem. Geol. 437, 67–76 (2016).ADS 
Article 

Google Scholar 
DeCarlo, T. M., Gaetani, G. A., Holcomb, M. & Cohen, A. L. Experimental determination of factors controlling U/Ca of aragonite precipitated from seawater: Implications for interpreting coral skeleton. Geochim. Cosmochim. Acta 162, 151–165 (2015).ADS 
Article 

Google Scholar 
Reeder, R. J., Nugent, M., Lamble, G. M., Tait, C. D. & Morris, D. E. Uranyl Incorporation into Calcite and Aragonite: XAFS and Luminescence Studies. Environ. Sci. Technol. 34, 638–644 (2000).ADS 
Article 

Google Scholar 
Anagnostou, E. et al. Seawater nutrient and carbonate ion concentrations recorded as P/Ca, Ba/Ca, and U/Ca in the deep-sea coral Desmophyllum dianthus. Geochim. Cosmochim. Acta 75, 2529–2543 (2011).ADS 
Article 

Google Scholar 
Chen, S., Littley, E. F. M., Rae, J. W. B., Charles, C. D. & Adkins, J. F. Uranium distribution and incorporation mechanism in deep-sea corals: Implications for seawater [CO32–] proxies. Front. Earth Sci. 9, 159 (2021).ADS 

Google Scholar 
Inoue, M., Suwa, R., Suzuki, A., Sakai, K. & Kawahata, H. Effects of seawater pH on growth and skeletal U/Ca ratios of Acropora digitifera coral polyps. Geophys. Res. Lett. 38, L12809 (2011).ADS 

Google Scholar 
Gothmann, A. M. & Gagnon, A. C. The primary controls on U/Ca and minor element proxies in a cold-water coral cultured under decoupled carbonate chemistry conditions. Geochim. Cosmochim. Acta 315, 38–60 (2021).ADS 
Article 

Google Scholar 
Mass, T. et al. Cloning and characterization of four novel coral acid-rich proteins that precipitate carbonates in vitro. Curr. Biol. 23, 1126–1131 (2013).PubMed 
Article 

Google Scholar 
Rogers, A. D. Advances in Marine Biology, Vol. 79 (ed Sheppard, C.) 137–224 (Academic Press, 2018).Rodolfo-Metalpa, R. et al. Coral and mollusc resistance to ocean acidification adversely affected by warming. Nat. Clim. Chang. 1, 308–312 (2011).ADS 
Article 

Google Scholar 
Hoarau, L. et al. Unexplored refugia with high cover of scleractinian Leptoseris spp. and hydrocorals Stylaster flabelliformis at lower mesophotic depths (75–100 m) on lava flows at Reunion Island (Southwestern Indian Ocean). Diversity 13, 141 (2021).Article 

Google Scholar 
Lindner, A., Cairns, S. D. & Cunningham, C. W. From offshore to onshore: Multiple origins of shallow-water corals from deep-sea ancestors. PLoS ONE 3, e2429 (2008).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Stewart, J. A. et al. Refining trace metal temperature proxies in cold-water scleractinian and stylasterid corals. Earth Planet. Sci. Lett. 545, 116412 (2020).Article 

Google Scholar 
Seacarb: Seawater Carbonate Chemistry. R package version 3.0.6 .http://CRAN.R-project.org/package=seacarb (2015).Lueker, T. J., Dickson, A. G. & Keeling, C. D. Ocean pCO2 calculated from dissolved inorganic carbon, alkalinity, and equations for K1 and K2: Validation based on laboratory measurements of CO2 in gas and seawater at equilibrium. Mar. Chem. 70, 105–119 (2000).Article 

Google Scholar 
Lee, K. et al. The universal ratio of boron to chlorinity for the North Pacific and North Atlantic oceans. Geochim. Cosmochim. Acta 74, 1801–1811 (2010).ADS 
Article 

Google Scholar 
Olsen, A. et al. The Global Ocean Data Analysis Project version 2 (GLODAPv2)—An internally consistent data product for the world ocean. Earth Syst. Sci. Data 8, 297–323 (2016).ADS 
Article 

Google Scholar 
Hemming, N. G. & Hanson, G. N. Boron isotopic composition and concentration in modern marine carbonates. Geochim. Cosmochim. Acta 56, 537–543 (1992).ADS 
Article 

Google Scholar 
Zeebe, R. E. & Wolf-Gladrow, D. A. CO2 in Seawater: Equilibrium, Kinetics, Isotopes Vol. 65 (Elsevier, 2001).
Google Scholar 
Foster, G. L., Pogge von Strandmann, P. A. E. & Rae, J. W. B. Boron and magnesium isotopic composition of seawater. Geochem. Geophys. Geosyst. 11, Q08015 (2010).ADS 
Article 

Google Scholar 
Klochko, K., Kaufman, A. J., Yao, W., Byrne, R. H. & Tossell, J. A. Experimental measurement of boron isotope fractionation in seawater. Earth Planet. Sci. Lett. 248, 276–285 (2006).ADS 
Article 

Google Scholar 
Stewart, J. A. et al. NIST RM 8301 boron isotopes in marine carbonate (simulated coral and foraminifera solutions): Inter-laboratory δ11B and trace element ratio value assignment. Geostand. Geoanal. Res. 45, 77–96 (2020).Article 

Google Scholar 
Foster, G. L. Seawater pH, pCO2 and [CO32−] variations in the Caribbean Sea over the last 130 kyr: A boron isotope and B/Ca study of planktic foraminifera. Earth Planet. Sci. Lett. 271, 254–266 (2008).ADS 
Article 

Google Scholar 
Schlitzer, R. Ocean Data View, Version 4.6.5 http://odv.awi.de, (2021). More

Analysis of changes in ecosystem services value in the YRBThe results showed that from 1990 to 2020, the total ecosystem services value in the YRB showed a dynamic trend of decrease-increase–decrease, with overall increasing trend, and a total increase of 31.85 × 1010 USD, with an average annual increase of 1.14 × 1010 USD (Table 2). This changing trend is consistent with land use cover change in the area. In 30a, YRB cultivated land decreased by 8663 km2, due to rapid urbanization. In addition, after year 2000, China began to implement the policy of returning farmland to forest and grassland on a large scale, which accelerated the reduction of cultivated land. Results again showed that the forest area increased by 30,933,093 km2, indicating that the implementation of “returning farmland to forest and grassland”policy achieved great results, thus increased the value of ecosystem services generated by forest land by 167.66 × 1010 USD. Grassland increased by 738 km2, as corresponding ESV increased by 28.73 × 1010 USD, while unused land decreased by 8131 km2, with 9.52 × 1010 USD ESV decrease. In general, the ecological protection and management measures in the YRB have achieved remarkable results, and ecosystem service values has been significantly improved due to forest and grassland increase.Table 2 The value of ecosystem services in the YRB from 1990 to 2020.Full size tableIn terms of ecosystem service structure in the YRB (Table 3), the relative proportions of various ESVs did not change significantly, resulting in relatively stable ESV structure. Soil conservation and waste disposal are the most important among them, accounting for about 37% of ESV’s total value. The YRB ecosystem, as can be seen, emphasises the importance of soil conservation and waste disposal in the basin, with Climate regulation, Biodiversity conservation, and Entertainment accounting for only 11.99 percent of the total. Various services have changed to varying degrees during the study period. Waste disposal and climate regulation, for example, have suffered losses of 22.23 × 1010 USD and 20.29 × 1010 USD, respectively.The rest of the services showed an upward trend, among which the value of the Food production service increased the most, which was 19.03 × 1010 USD, owing to the obvious increase of the forest land and grassland area in the YRB.Table 3 The value of individual ecosystem functions in the YRB from 1990 to 2020.Full size tableSpatial distribution and variation characteristics of ecosystem services in the YRBThe total ESV value of the study area and changes in the value of each service could not reflect their spatial differences. To describe the temporal and spatial distribution pattern of ESV in the study area, the natural breakpoint method was used. This method was further used to classify ESV with reference to existing studies, and divided the area into four levels: low-value, lower-value, higher-value, and high-value areas. Takin the three-level watershed of the YRB as the statistical unit for analysis, the result showed that the higher the level, the higher the ESV. As shown in Fig. 2, from 1990 to 2020, the spatial characteristics of ESV were relatively stable. The YRB’s upper reaches, from Shizuishan to the north bank of Hekou Town, the Fenhe River Basin, from Hekou Town to Longmen, and the Jinghe River Basin are all rich in high-values. The forest and grassland are relatively concentrated in the above-mentioned areas, the ESV coefficient is high, and the watershed area is large, resulting in a high total ESV. The higher value areas are mainly distributed in the areas from Longyang Gorge to Lanzhou main stream basin, the Daxia River and Tao River basin, and the Wei River basin. The area above Baoji Gorge and the inflow area fall in the transition zone between the high-value area and the lower-value area. For example, the transition area between the Loess and Qinghai-Tibet Plateaus is a higher-value area. The lower-value area mainly includes the Huangshui River Basin, the Datong River Basin, the basin below Lanzhou, and the Guanzhong Plain area. Thus, the unused land in this area is widely distributed. Due to the large area of construction land in the Guanzhong Plain, the ecosystem service value has shrunk. The low-value area is found in the YRB’s lower reaches, which contains the most extensive and large area of construction land in the basin, has a poor ecosystem service function, and is also the YRB’s most economically developed area. In terms of changes in the value of watershed ecosystem services, the number of watersheds at the ESV level did not change significantly between 1990 and 2020. The average ESV of the watershed is 40.52 × 1010 USD. There were 7 high-value, 5 higher-value, 12 lower-value, and 5 low-value watersheds respectively. Figure 2Spatial distribution of ESV changes in YRB from 1990 to 2020. (a) 1990, (b) 2000, (c) 2010, (d) 2020.Full size imageThe hotspot analysis revealed the spatial agglomeration characteristics and ESV evolution law in the YRB from 1990 to 2020 (Fig. 3). In most of the YRB, the ESV accumulation characteristics were not significant in space, and significant areas were dominated with high and low ESV accumulation. The Maqu-Longyangxia River Basin, Daxia River and Tao River Basin, the Datong River Basin, and Fen River Basin were the five core areas where ESV had the highest value. The Inner River, YRB’s northern and eastern margins, and the lower reaches are primarily low-value agglomeration areas. The high-value agglomeration area and low-value agglomeration area did not change significantly in space from 1990 to 2020, but the number of grids in each decreased from 647 to 627 and 699 to 681, respectively. In general, the YRB’s high-value agglomeration areas are strewn about, whereas the low-value agglomeration areas are scattered.Figure 3Spatial agglomeration characteristics of ESV in the YRB from 1990 to 2020. (a) 1990, (b) 2000, (c) 2010, (d) 2020.Full size imageFrom 1990 to 2020, the barycenter coordinates of the ESV in the YRB remained stable between 106.78°–106.94° E and 36.40°–36.65° N (Fig. 4). During the study period, the ESV barycenter coordinates showed a transfer trajectory of first to southwest, then to northeast, and then to southwest. From the perspective of overall transfer direction, ESV barycenter shifted from northeast of Huanxian County to southwest from 1990 to 2020. The ESV in the northeast decreased, while that in southeast increased. From 1995 to 2000 and from 2000 to 2005, the migration distance of ESV barycenter in the YRB was longer by 16.33 km and 15.75 km, respectively, while the barycenter migration distance of ESV from 2005 to 2020 was shorter.Figure 4Barycenter coordinates of ecosystem services in the YRB from 1990 to 2020.Full size imageResponse of ecosystem services to land-use changeThe area of land use type change in the YRB increased by 64,356 km2 between 1990 and 2020. Each land type’s area has changed to varying degrees. Cultivated land and construction land are the two land types that have seen the most changes. The area of cultivated land has shrunk by 8663 km2, while the area of construction land has grown by 13,109 km2. In comparison to water, forest, and grassland, unused land has undergone significant transformations. However, in comparison to 1990, it shrunk by 8131 km2 in 2020. The forest increased by 3093 km2 while grassland increased by 738 km2. Ecosystem services are significantly impacted by changes in land use types. Using the spatial analysis method, the researcher introduces a resilience index to reflect ESV’s response to land-use change in this paper. During 1990–2000 and 2000–2010, average elasticity of ESV change in the YRB relative to land use change was 0.27 and 0.44, respectively, but dropped to 0.04 during 2010–2020. This indicates that the disturbance capacity of land-use change on ecosystem services was low between 1990 and 2000, but increased between 2000 and 2010. Land-use change has had less of an impact on ecosystem services since 2010. The range of changes in land land-use types was wide during this time, but the average elasticity index was low because there were so many different types of land land-use changes, such as the conversion of forest land and cultivated land to construction land, and the conversion of forest land and water area to cultivated land. The decrease in ESV caused by the change in land use per unit area was minor. Furthermore, the forest land and grassland in the river basin have been effectively increased, as ESV has increased. Overall, the value of ecosystem services has remained relatively constant.Accurate spatial statistics on the elasticity index from 1990 to 2020 was carried out (Fig. 5). The elastic index of the upper YRB and Loess Plateau is higher, and the impact of land use change on ecosystem services is more apparent in this region, according to the findings. This is mainly due to the implementation of large-scale ecological engineering measures in response to vegetation degradation in the upper reaches of the YRB and soil erosion in the middle reaches (Loess Plateau), by the Chinese government. In addition, Lanzhou New District, Guanzhong Plain, and the lower Yellow River region also showed higher elasticity index. The above-mentioned regional development and construction, as well as human activities, have resulted in a rapid increase in construction land, resulting in a significant decline in ecosystem services and a higher resilience index as a result of rapid urbanisation.Figure 5Spatial distribution of elastic coefficients in the YRB from 1990 to 2020.Full size imageIn general, the land use types in the YRB have changed dramatically, and land type conversion is very common. The conversion of ecological land to urban construction land, as well as the conversion of unused and cultivated land to ecological land, has resulted in significant changes in ecosystem service value. This demonstrates that the basin’s ecological construction projects have yielded positive environmental results. More

Global fire activity is changing in many areas as temperatures increase and land use intensifies1,2,3,4,5. This is sparking an increase in attention given to fire activity and fire ecology. However, the availability of data for spatially delineated fire events is limited or non-existent in many countries6, with most global fire data coming from satellite-based active fire detections7,8 and gridded burned area products9,10. The lack of products containing delineated events has led to many global studies about fire ecology that are computationally-intensive, coarse-scale trend analyses1,4.A key advantage of datasets like Monitoring Trends in Burn Severity (MTBS)11 or the Fire Occurrence Dataset12 lies in their ease of use. Since its inception in 2007 MTBS has been cited 947 times in peer-reviewed studies according to a Google Scholar search at the time of this writing, despite documented limitations for scientific use of some facets of the product13. The MTBS dataset is regularly updated, easy to find on the internet, and it is free, fast and easy to download and use. Many environmental scientists and resource managers do not have the computational budget or expertise in big data or remote sensing to deal with the challenges one must overcome to process large fire datasets. This is especially true for cases when all that is needed is a shapefile of fire perimeters that can be used to map fire history. Other global fire perimeter datasets have been produced from satellite-derived burned area products14,15, but these are only available in yearly or monthly global shapefiles. Often field-based studies of fire effects require an entire time series over study areas that are only a few hundred km in diameter16 or a single ecoregion17. The end user who wants to understand the fire history for their region would have to download yearly shapefiles with a global extent, clip all of those shapefiles to their area of interest, and then combine them into one shapefile, just to get started. We suspect that the lack of accessible fire perimeter datasets that are easy to download and use contributes to a disparity in research, where fire ecology studies are conducted mostly in developed countries that have either research infrastructure capable of handling big data or longer-term government records, or temperate forested regions that have substantial tree-ring records18.There are two existing global perimeter products, the Global Fire Atlas (GFA) (Andela et al.14) and the Global Wildfire Information System (GWIS) (Artes et al.15). Both were created by applying spatiotemporal flooding algorithms to the MODIS MCD64 Burned Area Product. These algorithms assign burned pixels from the MCD64 products using a moving window whose size is defined by spatial and temporal parameters. They are created as monthly or yearly slices of the entire globe, and they can be subsetted. These products are extremely valuable for global scale studies. But when we look at how those products delineate known fire events we see a consistent problem in that they both seem to over-segment events in ways that appear unrealistic. This inconsistent event delineation is not problematic for coarse-scale or regional estimates of burned area or fire seasonality, but can lead to unrealistic estimates for number of fire events and event-level characteristics like fire size and spread rate. In Fig. 1 we illustrate this with an example of the 2013 Rim Fire in California, United States, which was unmistakably a single event that burned about 90,000 ha over the course of three months. Figure 2 illustrates how the day-to-day progression of the Rim Fire was a steady progression from a single ignition in late August. Table 1 shows how the differences in event delineation propagate to calculations of burned area and number of events. In the GFA, the Rim Fire is delineated as one large event of 804.5 km2, and 13 additional events totaling 88.7 km2. in GWIS it is delineated as one event of 878 km2 and 47 additional events totalling 20 km2. With FIRED, there is one event of 892 km2 and 2 single pixel events totalling less than one km2. One cause for potential differences is how one defines a “fire event”. Large fires often have multiple ignition sources. The Global Fire Atlas algorithm and others19, for example, search for local minima to identify various ignition locations that may begin as small patches, only to later form a large complex and in the end described with a single fire perimeter. The choice of outside sources for optimizing the spatial-temporal parameters, the method of optimization, and the intent of the final product’s meaning (defining events as single ignition patches vs contiguous burned area) all lead to different outcomes in the final events that are delineated. Another likely source of this discrepancy is that GWIS and GFA are calibrated to create a single global product. Because different geographical areas have different types of fire regimes, they have fires that grow at different rates and to different sizes, and occur in greater or fewer frequencies, and so the spatial and temporal parameters that work well for defining a fire event in one area may result in over- or under-segmentation in other areas. Here, we decided upon an approach of creating many regional products across the globe, rather than one product for everywhere on earth.Fig. 1Comparison of global fire event products performance for the 2013 Rim Fire (a). In the FIRED product (b), the Rim fire was classified as one very large event with two single pixel events. The Global Fire Atlas (GFA, c) and Global Wildfire Information System (GWIS, d) each delineated a very large event, with 13 and 47 smaller events, respectively.Full size imageFig. 2The two primary outputs FIREDpy provides are a daily- and event-level product. Panel a shows the default single event polygon. In b, each day has a separate polygon, with associated statistics generated, within each event. Panel c shows the daily perimeters derived from the airborne infrared by the incident management team for comparison.Full size imageTable 1 Rim fire comparison.Full size tableBesides the ease of access and use, the advantage of the FIRED product lies in the user’s ability to use the open-source software, FIREDpy, to tailor the spatial and temporal parameters of the moving window algorithm in order to realistically delineate events for their region of interest. In Fig. 3, we illustrate this by comparing the three products for a pair of small fires in Florida. In this case, the FIRED product that was created with a larger moving window (5 pixels and 11 days) over-aggregated the events, but it only required one line of code at command line to recreate the product with a smaller moving window (1 pixel and 5 days) to get more realistic results.Fig. 3Product comparison for two small events in Florida, the Moonshine Bay and Sour Orange fires (outlined) that both ignited in February of 2007 and were delineated by MTBS. In b the firedpy product that was optimized for the entire United States with a moving window of 5 pixels, 11 days resulted in aggregation of the two fires delineated by MTBS, but also several smaller fires nearby. In b, it was re-ran with a window of one pixel and five days, for a more realistic result. Delineations by the Global Fire Atlas (c) and the Global Wildfire Information System (d) are shown for comparison.Full size imageHere, we present a collection of regionally-tailored fire perimeter datasets for every country in the world with significant fire activity20, which we created with the open source algorithm, FIREDpy21. Each dataset is either a single country or a broader region, depending on the data volume. These datasets differ from other similar efforts14,15 in that each dataset created by FIREDpy is a single file containing a collection of polygons that is generated for the entire time series, rather than monthly or yearly aggregations with a global extent. Furthermore, we have generated the data products at a spatial extent land managers and ecologists would typically use to do regional-scale research, and we adjusted the spatial and temporal parameters for each country to yield realistic event delineations. We also made every effort to ensure that download sizes are reasonable (  More

Klein, A. M. et al. Importance of pollinators in changing landscapes for world crops. Proc. R. Soc. B. 274, 303–313 (2007).PubMed 
Article 

Google Scholar 
IPBES. The assessment report of the intergovernmental science-policy platform on biodiversity and ecosystem services on pollinators, pollination and food production. in Secretariat of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services, Bonn, Germany (Potts, S.G., Imperatriz-Fonseca, V.L., Ngo, H.T. eds.). 1–552. https://ipbes.net/sites/default/files/downloads/pdf/individual_chapters_pollination_20170305.pdf (2016).Ollerton, J. et al. How many flowering plants are pollinated by animals?. Oikos 120, 321–326 (2011).Article 

Google Scholar 
Linder, H. P. Morphology and the Evolution of Wind Pollination. Reproductive Biology 123–135 (Royal Botanic Gardens, 1998).
Google Scholar 
Friedman, J. & Barrett, S. C. H. Wind of change: New insights on the ecology and evolution of pollination and mating in wind-pollinated plants. Ann. Bot. 103, 1515–1527 (2009).PubMed 
PubMed Central 
Article 

Google Scholar 
Gallai, N. et al. Economic valuation of the vulnerability of world agriculture confronted with pollinator decline. Ecol. Econ. 68, 810–821 (2009).Article 

Google Scholar 
Potts, S. G. et al. Safeguarding pollinators and their values to human well-being. Nature 540, 220–229 (2016).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Srinivasan, M. R. et al. Impact of Pesticides on Honey Bees and Pollinators. Pesticide Application in Agro Ecosystem-Its Dynamics and Implications 243–248 (TNAU Publications, 2015).
Google Scholar 
Sanchez-Bayo, F. & Goka, K. Impacts of Pesticides on Honey Bees. Beekeeping and Bee Conservation—Advances in Research. https://doi.org/10.5772/62487. (InTech, 2016).Berry, I. Dead bees don’t pollinate. Orchardist. New Zealand, 60, 287 (1987). Rev. Appl. Entomol. Ser. A 76, 1087 (1998).
Google Scholar 
Chandrasekaran, S. et al. Disposed paper cups and declining bees. Curr. Sci. 101(10), 1262 (2011).
Google Scholar 
Sandilyan, S. Decline in honey bee population in Southern India: Role of disposable paper cups. J. Zool. Biosci. Res. 1, 6–9 (2014).
Google Scholar 
Allen-Wardell, G. et al. The potential consequences of pollinator declines on the conservation of biodiversity and stability of food crop yields. Conserv. Biol. 12, 8–17 (1998).Article 

Google Scholar 
FAO. Declining Bee Populations Pose Threat to Global Food Security and Nutrition. UN World Bee Day, 20 May, Rome. https://www.fao.org/news/story/en/item/1194910/icode/. (2019).Najaran, Z.T. et al. Dill (Anethum graveolens L.) Essential Oils in Food Preservation, Flavor and Safety. https://doi.org/10.1016/C2012-0-06581-7 (Academic Press, 2016). Khare, C.P. Indian Herbal Remedies: Rational Western Therapy, Ayurvedic, and Other Traditional Usage, Botany. 1st edn. 326–327. (Springer, 2004).Jana, S. & Shekhawat, G. S. Anethum graveolens: An indian traditional medicinal herb and spice. Pharmacogn. Rev. 4, 179–184 (2010).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Biesiada, A. et al. Nutritional value of garden dill (Anethum graveolens L.), depending on genotype. Notulae Bot. Horti Agrobot. Cluj-Napoca 47, 784–791 (2019).CAS 

Google Scholar 
Pulliah, T. Medicinal Plants in India. Vol. 1. 55–56. (Regency Publications New Delhi, 2002).Hornok, L. Cultivation and Processing of Medicinal Plants. 338. (Academic Publications, 1992).Nair, R. & Chanda, S. Antibacterial activities of some medicinal plants of the western region of India. Turk. J. Biol. 31, 231–236 (2007).
Google Scholar 
DASD. State Agriculture/Horticulture Departments/DASD Kozhikode, Kerala. https://www.dasd.gov.in/index.php/content/index/statistics (2020).Nemeth, E. & Szekely, G. Floral biology of medicinal plants I. Apiaceae species. Int. J. Horticult. Sci. 6, 133–136 (2000).
Google Scholar 
Weiss, E. A. Spice Crops. 268–283 (CAB International, 2002).Book 

Google Scholar 
Peter, K.V. Dill in Handbook of Herbs and Spices (Gupta, R., Answer, M.M., Sharma, Y.K. Eds.). 275–285. (Woodhead Publishing Limited, 2012).Meena, N. K. et al. Role of insect pollinators in pollination of seed spices—A review. Int. J. Seed Spices 5, 1–17 (2015).
Google Scholar 
Faegri, K. & van der Pijl, L. The Principles of Pollination Ecology 3rd edn. (Pergamon, 1980).
Google Scholar 
Ali, M., Saeed, S., Sajjad, A. & Whittington, A. In search of the best pollinators for canola (Brassica napus L.) production in Pakistan. Appl. Entomol. Zool. 46, 353–361 (2011).Article 

Google Scholar 
Singh, H., Swaminathan, R. & Hussain, T. Influence of certain plant products on the insect pollinators of coriander. J. Biopest. 3, 208–211 (2010).
Google Scholar 
Kant, K. et al. Relative abundance and foraging behavior of honey bee species on minor seed spice crops. Int. J. Seed Spices 3, 51–54 (2013).
Google Scholar 
Willmer, P. G. et al. The superiority of bumblebees to honeybees as pollinators: Insect visits to raspberry flowers. Ecol. Entomol. 19, 271–284 (1994).Article 

Google Scholar 
Stone, J. L. Components of pollination effectiveness in Psychotria suerrensis, a tropical distylous shrub. Oecologia 107, 504–512 (1996).ADS 
PubMed 
Article 

Google Scholar 
Olsen, K. M. Pollination effectiveness and pollinator importance in a population of Heterotheca subaxillaris (Asteraceae). Oecologia 109, 114–121 (1997).ADS 

Google Scholar 
Ivey, C. T. et al. Variation in pollinator effectiveness in swamp milkweed, Asclepias incarnate (Apocynaceae). Am. J. Bot. 90, 214–225 (2003).PubMed 
Article 

Google Scholar 
Korpela, S. The influence of honeybee pollination on turnip rape (Brassica campestris) yield and yield components. Ann. Agric. Fenniae 27, 295–303 (1988).
Google Scholar 
Sabbahi, R. et al. Influence of honey bee (Hymenoptera: Apidae) density on the production of canola (Cruciferae: Brassicacae). J. Econ. Entomol. 98, 267–372 (2005).Article 

Google Scholar 
Warakomska, Z. et al. Biology of the bloom and pollination of the umbelliferous vegetables. Part 1: garden dill (Anethum graveolens L.). Acta Agrobot. 35, 69–78 (1982).Article 

Google Scholar 
Meena, N. K. et al. Pollinator’s diversity and abundance on cumin (Cuminum cyminum L.) and their impact on yield enhancement at semi-arid region. J. Entomol. Zool. Stud. 6, 1017–1021 (2018).
Google Scholar 
Malhotra, S.K. & Vashishtha, B.B. Package of practices for production of seed spices. in Book Published by the Director, ICAR-National Research Centre on Seed Spices, Ajmer. 71–79. (2008).Chaudhary, O. P. diversity, foraging behaviour of floral visitors and pollination ecology of fennel (Foeniculum vulgare Mill). J. Spices Aromatic Crops 15, 34–41 (2006).
Google Scholar 
Rianti, P. et al. Diversity and effectiveness of insect pollinators of Jatropha curcas L. (Euphorbiaceae). HAYATI J. Biosci. 17, 38–42 (2010).Article 

Google Scholar 
Choi, S. W. & Jung, C. Diversity of insect pollinators in different agricultural crops and wild flowering plants in korea: Literature review. J. Apicult. 30, 191–201 (2015).MathSciNet 
Article 

Google Scholar 
Siregar, E. F. et al. Diversity and abundance of insect pollinators in different agricultural lands in Jambi, Sumatera. HAYATI J. Biosci. 23, 13–17 (2016).Article 

Google Scholar 
Devi, M. et al. Diversity of insect pollinators in reference to seed set of mustard (Brassica juncea L.). Int. J. Curr. Microbiol. Appl. Sci. 6, 2131–2144 (2017).Article 

Google Scholar 
Martin, P. & Bateson, P. Measuring Behaviour: An Introductory Guide. 2nd edn. (Cambridge University Press, 1993).Dafni, A. Pollination Ecology: A Practical Approach (Oxford University Press, 1992).
Google Scholar 
Chaudhary, O. P. & Singh, J. Diversity, temporal abundance, foraging behaviour of floral visitors and effect of different modes of pollination on coriander (Coriandrum sativum L.). J. Spices Aromatic Crops 16, 8–14 (2007).
Google Scholar 
Kulkarni, S. R., Gurve, S. S. & Chormule, A. J. Effect of different indigenous bee attractants in onion (Allium cepa L.) crop. Ann. Plant Protect. Sci. 25, 78–82 (2017).
Google Scholar 
Manhare, J. S. & Painkra, G. P. Impact of bee attractants on bee visitation on buckwheat (Fagopyrum esculentum L.) crop. J. Entomol. Zool. Stud. 6, 28–31 (2018).
Google Scholar 
Kapas, A. et al. The kinetic of essential oil separation from fennel by microwave assisted hydro-distillation (MWHD). UPB Sci. Bull. Ser. B 73, 113–120 (2011).CAS 

Google Scholar 
Warrier, P. K. et al. Indian Medicinal Plants. Vol. 1. 153–157. (Orient Longman Limited, 1994).Baswana, K. S. Role of insect pollination on seed production in coriander and fennel. South Indian Horticult. 32, 117–118 (1984).
Google Scholar 
Koul, A. K. Pollination mechanism in Coriandrum sativum L. (Apiaceae). Proc. Indian Acad. Sci. Plant Sci. 99, 509–515 (1989).Article 

Google Scholar 
Narayana, E. S., Sharma, P. L. & Phadke, K. G. Insect pollinators of saunf (Foenicuum vulgare) with particular reference to the honeybees at Pusa (Bihar). Indian Bee J. 22, 7–13 (1960).
Google Scholar 
Mukherjee, S. et al. Pollination events in Nigella sativa L. black cumin. Int. J. Res. Ayurveda Pharm. 4, 342–344 (2013).Article 

Google Scholar 
Abrar, M. et al. Insect pollinators and their relative abundance on black cumin Nigella sativa L. at Dera Ismail Khan. J. Entomol. Zool. Stud. 5, 1252–1258 (2017).
Google Scholar 
Ollerton, J. & Louise, C. Latitudinal trends in plant-pollinator interactions: Are tropical plants more specialized?. Oikos 98, 340–350 (2002).Article 

Google Scholar 
Meena, N. K. et al. Diversity of floral visitors and foraging behavior and abundance of major pollinators on fennel under semi-arid conditions of Rajasthan. Int. J. Trop. Agric. 34, 1891–1897 (2016).
Google Scholar 
Sikdar, S. et al. Diurnal foraging activity of flower visiting insects on some seed spices under terai agro-climatic zone of West Bengal. J. Entomol. Zool. Stud. 7, 299–303 (2019).
Google Scholar 
Kapil, R. P. et al. Integration of bee behaviour with aphid control for seed production of Brassica campestris var. toria. Indian J. Entomol. 33, 221–223 (1971).
Google Scholar 
Bhalla, O. P. et al. Insect visitors of mustard bloom Brassica campestris var sarson, their number and foraging behavior under mid-hill conditions. J. Entomol. Res. 1, 15–17 (1983).
Google Scholar 
Rao, G. M. & Suryanarayana, M. C. Studies on the foraging behaviour of honeybees and its effect in seed yield of niger. Indian Bee J. 52, 31–33 (1990).
Google Scholar 
Abrol, D. P. Foraging behavior of Apis mellifera L. and A. cerana F. as determined by the energetics of nectar production in different cultivars of Brassica campestris var toria. J. Apicult. Sci. 51, 19–24 (2007).
Google Scholar 
Inouye, D. W. The effect of proboscis and corolla tube lengths on patterns and rates of flower visitation by bumble bees. Oecologia 45, 197–201 (1980).ADS 
PubMed 
Article 

Google Scholar 
Vicens, N. & Bosch, J. Pollination efficacy of Osmia cornuta and Apis mellifera (Hymenoptera: Megachilidae, Apidae) on ‘Red Delicious’ apple. Environ. Entomol. 29, 235–240 (2000).Article 

Google Scholar 
Singh, J. et al. Foraging rates of different Apis species visiting parental lines of Brassica napus L. Zoos’ Print J. 21, 2226–2227 (2006).Article 

Google Scholar 
Engel, E. C. & Irwin, R. E. Linking pollinator visitation and rate of pollen receipt. Am. J. Bot. 90, 1612–1618 (2003).Article 

Google Scholar 
Sihag, R. C. Insect pollination increase seed production in cruciferous and umbelliferous crops. J. Apic. Res. 25, 121–126 (1986).Article 

Google Scholar 
Verma, S. & Dwivedi, S. N. Floral biology of Trachyspermum ammi (Linn.) Spr. Inventi rapid. Planta Activa 2, 1–6 (2018).
Google Scholar 
Singh, B. Effectiveness of different pollinators on yield and quality of greenhouse grown tomatoes and melons: A review. Haryana J. Horticult. Sci. 31, 245–250 (2002).ADS 

Google Scholar 
Biswanath, B. et al. Role of insect pollinators in seed yield of coriander (Coriandrum sativum L.) and their electroantennogram response to crop volatiles. Agric. Res. J. 54, 227–235 (2017).Article 

Google Scholar 
Giannini, T. C. et al. The dependence of crops for pollinators and the economic value of pollination in Brazil. J. Econ. Entomol. 108, 849–857 (2015).CAS 
PubMed 
Article 

Google Scholar  More

Case study areaThe studied catchment (2 621 km2) is located in the central-western part of Poland, and constitutes a part of the Oder River basin. The Wełna River (118 km) discharges to the Warta River near the town of Oborniki18, with an average flow rate of 8.1 m3s−1 (1980–2019) in this profile19. The natural conditions in this catchment favour the development of intensive agriculture, which covers almost 72% of this area (1888 km2) and contributes to the high consumption of mineral fertilizers20. Forest areas cover another 22% of this catchment (589 km2), while urbanised ones only 4% (93 km2) (Fig. 1). The Wełna River catchment is inhabited by approx. 230,000 people, of which only approx. 74% is served by wastewater treatment facilities21.Figure 1Localisation of the Wełna River catchment with its land use forms and nutrient sources. This figure was created using ArcGIS 10.2.1 for Desktop available at https://www.esri.com/en-us/home. Licence granted to Institute of Meteorology and Water Management.Full size imageInput dataBoth the mass-balance method and the modelling method require a similar amount and type of input data (Supplementary Table S1). Basic information on the Wełna River daily flow rates and nutrient concentrations in the closing profile of the catchment (Oborniki) has been obtained from the state monitoring services (Institute of Meteorology and Water Management—National Research Institute—IMGW-PIB13 and State Environmental Monitoring22—SEM) (Supplementary Table S1). They have formed the basis for the estimation of the share of individual sources in the mass-balance method, as well as for the calibration of the Macromodel DNS/SWAT in the modelling method. Other data, such as maps of elevation, river network and soil maps, as well as meteorological data, necessary for the development of an accurate representation of the studied catchment area on the Macromodel DNS/SWAT digital platform, were also obtained from state repositories. Data on the land use comes from the Corine Land Cover8, while detailed information on nutrient sources has been obtained mostly from the Local Data Bank of statistical information. The utilisation of the collected database has been presented in Fig. 2, and described in the following text. The comparison of the results for nutrient loads from both method was based on the year 2017, which was characterised by the maximum amount of monitoring data for both flows (365 measurements) (IMGW-PIB) and total nitrogen (TN) and total phosphorus (TP) (12 measurements–SEM). The average air temperature in 2017 in Poland was 1.5 °C higher than the long-term average (1971–2000) and was over 10 °C which resulted from the warm autumn and the end of the year. The time of the snow cover presence was shorter than the long-term data, and the rest of the year was classified as thermally normal.Figure 2Methodology diagram with relevant chapters marked in grey ovals (green—steps and data used for Mass Balance method, blue—steps data used for Modelling method, green/blue—steps and data used for both methods).Full size imageIn terms of precipitation, 2017 was assessed as wet, similarly due to rainy autumn and summer. In the Wełna River catchment area, the annual rainfall was about 770 mm, however high variability of precipitation conditions in particular months, from extremely wet to very dry, should be noted23. Therefore hydrologically, 2017 was considered normal with the flows only slightly lower than the long-term average.Mass-balance methodThe first method used for the quantification of sources and loads in the studied area was the static mass-balance method. It is widely used by the Polish administration authorities responsible for water management17. This method is based on the assumption that the sum of the nutrient loads in the river’s closing profile (selected based on access to the monitoring data) and its retention in the catchment equals the emission of nutrients in a given time. Such assumption allows the apportioning of the river loads among identified sources and the estimation of their contribution to the total loads, based on known or assumed values of their retention.River load calculationThe total load of nutrients discharged from the catchment was calculated using the daily flow rate and nutrient concentrations in the closing profile of the catchment area (Oborniki, Fig. 1) from the SEM (Supplementary Table S1). The daily river load was calculated using the following Eq. 5:$${L}_{river}=0.0864sum_{t=1}^{n=365}{({Q}_{t}cdot {C}_{t})}_{t}$$
(1)
where: Lriver is the annual load [kga-1], n is the number of days, t is the consecutive day, Ct is the concentration [mg L-1], Qt is the mean daily flow rate [Ls-1], and 0.0864 is the unit conversion.Due to the fact that the flow rate is measured daily and nutrient concentrations only 12 times a year, the linear interpolation method5 was used to obtain the daily concentration values:$${x}_{k}={x}_{a}+kcdot frac{{x}_{b}-{x}_{a}}{n+1}$$
(2)
where: xk is the interpolated concentration value, xa is the first of the two measured concentration values between which the concentrations are interpolated, xb is the second of the two measured concentration values between which the concentrations are interpolated, k is the consecutive number of missing value and n is number of missing values.Source apportionmentFor the mass-balance method, data on nutrient loads for source apportionment (emission inventory) was collected in order to proceed with further calculations. The calculations were performed for 2017, due to the availability of river monitoring data and the nutrient sources were divided into 7 categories, based on the HELCOM guidelines5: municipal (MWS) and industrial (INS) point sources, municipal diffuse sources (SCS), forestry (MFS), agriculture (AGS), natural background (NBS) and atmospheric deposition (ATS). The category of “unknown sources” (UKS) was taken into account, in order to include possible discrepancies in nutrients load apportionment, and to cover eventual differences between calculated river load and inventoried emission.The MWS loads were calculated on the basis of the number of inhabitants served by the wastewater treatment plants (WWTPs)21. In the Wełna River catchment, 151 771 inhabitants were served by the 12 WWTPs covered by the National Wastewater Treatment Program (NWTP)24, which provides information on the total discharge volume from each facility. For 5 of these plants, information on influent/effluent nutrient concentrations was also available, allowing the direct calculation of discharged loads. For the remaining seven facilities, the loads were calculated on the basis of the mean influent concentration information, available for the WWTPs covered by the NWTP (80 mgL−1 and 12 mgL−1 for TN and TP, respectively), and approximated nutrient reduction level in non-biological WWTPs. This reduction level, based on data from the NWTP, was set at 65% for TN and 35% for TP24. Another 19 350 inhabitants of this catchment were connected to the small WWTPs, not included in the NWTP. This part of the MWS load was calculated using the mean daily wastewater outflow (0.12 m3day−1 per person), the same mean nutrient concentrations and reduction levels as presented above. Additionally, the remaining 25% of the catchment’s population (58,000) is not connected to any WWTP and uses septic tanks and other types of individual wastewater treatment systems. The load from this source was expressed as SCS, and calculated using unit loads set on 11 gday−1 per person and 1.6 gday-1 per person for TN and TP, respectively17. The industrial nutrient input information (INS) was gathered directly from the Statistics Poland office database21.The AGS load was calculated using nitrate and phosphate concentrations in shallow groundwater (90 cm below the ground surface), from 22 sampling points located on agricultural areas in the Wełna River catchment17. Concentrations were recalculated to TN and TP respectively and averaged. Thus, the obtained mean concentrations were 8.25 mgL−1 of TN and 1.92 mgL−1 of TP. Subsequently, load values were calculated by multiplying these concentrations by the outflow from agricultural areas, calculated as a share of the total catchment outflow respective to the agricultural use of the area. The calculated loads were multiplied by coefficients reflecting the share of monitored outflow (groundwaters and tile drainage) from the agricultural runoff (1.11 for TN and 4.17 for TP)25. Subsequently, the natural background (NBS) was subtracted from the AGS load.The load corresponding to NBS was calculated using the total catchment outflow and nutrient concentration values reflecting conditions in undisturbed areas of pre-human activity, set as 0.15 mgL−1 and 0.02 mgL−1, for TN and TP respectively17. The MFS load was also calculated in a similar way, using nutrient concentrations set to represent forest catchment as 0.31 mgL−1 and 0.038 mgL−117 and the outflow calculated as the share of the total catchment area, respective for the catchment part covered by forest. Also in this case, the NBS load has been subtracted. As for the ATS load, data on pollutant deposition into the ground from precipitation was taken from the SEM network26. This data was based on precipitation and its chemistry measurements taken from 22 monitoring stations covering the entire territory of Poland. The total load from the point and diffuse sources was calculated by adding the loads mentioned above. The eventual difference between the river load (“River load calculation” Section) and inventoried emission (“Mass-balance method” Section) accounted for the other sources (UKS).Load apportionmentThe contribution of each source to the calculated river load was calculated based on a simplified equation modified from HELCOM5:$${L}_{river}=DP+LOD-RP-RD$$
(3)
where: Lriver is the river load [kga−1], DP is the load from point sources (MWS and INS) [kga−1], LOD is the load from diffuse sources (SCS, ATS, MFS, AGS and, NBS) [kga−1], RP is the point source retention [kga−1] and RD is the diffuse source retention [kga−1].In the adopted mass-balance method, it is assumed that nutrient load from the point sources (DP) is introduced directly into the river bed phase, while load from the diffuse sources (LOD) is discharged into both phases of the catchment, land and river bed ones. In both phases, self-purification processes are taking place, resulting in the reduction of nutrient loads on the way from the source to the catchment closing profile. However, due to the limited amount of data, the self-purification processes in the river have been omitted, therefore the point source retention (RP) equalled 0 kga−1. Subsequently, the diffuse source retention (RD) has been estimated on the basis of the difference between each nutrient load of the river (Lriver) and the point sources (LOD). The remaining river load has been then attributed proportionally to the contribution of the particular diffuse sources to the total source apportionment (emission inventory).Modelling methodThe digital platform, the Macromodel DNS with the SWAT module27,28,29,30,31,32, was used for comparison for the nutrient balancing method described in “Mass-balance method” Section. This advanced dynamic tool tracks nitrogen and phosphorus migration paths in the river basin taking into account their spatial and temporal variability. For this purpose, it takes into account a very extensive input database, similar to that used in the mass balance method (Supplementary Table S1). Natural and anthropogenic processes that affect the transport and transformation of nutrients, are also part of this platform. The SWAT module (version 2012) is a tool which operates in the spatial information system (GIS) and is fully integrated with it. Using the digital elevation model (DEM), the SWAT module divided the entire analysed Wełna River catchment into a total of 225 sub-catchments of an average area of 11.5 km2. The subsequent use of data on land use (forests, agriculture and urbanised areas) and the types of soils (31 classes) allowed the authors to identify a total of 2824 hydrological response units (HRUs), homogeneous in terms of vegetation, soil and topography33. Afterwards, a simulation of soil water content, evapotranspiration, surface runoff, primary and underground flows was carried out in accordance with the water balance Eq. (4), which represents the basis for the quantitative component and the HRU.$${SW}_{t}={SW}_{0}+sum_{i=1}^{t}({R}_{day}-{Q}_{surf}-{E}_{a}-{W}_{seep}-{Q}_{gw})$$
(4)
where: SWt is the final soil water content (mm H2O), SW0 is the initial soil water content (mm H2O), Rday is the amount of precipitation (mm H2O), Qsurf is amount of surface runoff (mm H2O), Ea is the amount of evapotranspiration (mm H2O), Wseep is the amount of water entering the vadose zone from the soil profile (mm H2O), Qgw is the amount of return flow (mm H2O).The model directs all runoff flows generated by each HRU through the channel network, thus simulating a catchment. The water balance equation also represents a basis for the simulation, transport and transformation of nutrients required for the quantitative component of the model. This tool models forms of nitrogen, organic and inorganic , different forms of phosphorus in soil34, as well as organic nitrogen and phosphorus forms associated with plant residues, microbial biomass and soil humus35,36,37,38. Final results of simulations are produced by the SWAT model as all the forms of nitrogen and phosphorus (in kilograms of N and P per a time unit, respectively) are then summed up to give TN and TP values. To verify that the model properly predicts TN and TP values its results are calibrated with the TN and TP values resulting from SEM, as described in Sect. 2.4.1. Moreover, the particular forms of nitrogen and phosphorus have also been compared with the modelling results (Supplementary Table S4). A detailed overview of the migration and transformation pathways of nitrogen and phosphorus forms in the catchment has been presented in the Supplementary Information (Sect. S1), while mathematical description of these processes is included in the theoretical documentation of the SWAT model39.Similarly, as in the case of the mass-balance method, diffuse sources of nutrients from agriculture (AGS), forestry (MFS) or urban areas (URB) in SWAT were simulated in the land phase of the catchment. In the land phase, the model simulates both the infiltration of nutrients into the soil (fertilization, plant biomass, precipitation) and their removal from it (volatilization, denitrification, erosion, surface runoff). Additionally, changes in the distribution of nutrients in the soil (uptake by plants) and the low mobility of phosphorus itself are also taken into account39,40,41.Pollutants from municipal and industrial point sources (MWS, INS) are introduced directly into the river bed phase. The exception here is the nutrient load from municipal diffuse sources (SCS) which, reduced as a result of the self-purification processes taking place in the land phase, is also treated in the model as point sources. The SCS nutrient load mainly derives from leaking or illegally emptied septic tanks. For this purpose, septic tanks have been divided into three types: leaky, partially illegally emptied, and sealed septic tanks, legally emptied. The loads from the legally emptied tanks are included in the effluents from WWTPs reported in the catchment. While for the remaining types, their loads are calculated using factors depending on their effectiveness in nutrient removal (15 – 50%). The final nutrient load derived from these types of facilities is then calculated, taking into consideration the number of inhabitants using the different types of septic tanks and the average chemical composition of wastewater21.The load of nutrients from the atmospheric deposition (ATS) affects both land and river phases due to the presence of two deposition mechanisms in the SWAT module, i.e., wet and dry deposition. The model also allows for the determination of nutrient loads generated as a result of natural processes of nitrogen and phosphorus transformation and transport in the soil, with the omission of all anthropogenic pressure—natural background (NBS).Calibration, verification and validationThe SWAT module for the Wełna River has been calibrated, verified and validated using the SWAT-CUP software42. For the quantitative component (water circulation in the catchment), the implemented daily flow data (source: IMGW-PIB) for the period of 18 years (2001–2018) came from the water gauge stations on the Wełna River (Pruśce and Kowanówko) and its tributary (the Flinta River-Ryczywół) (Fig. 1). The qualitative component (nitrogen and phosphorus concentration in the catchment) was gathered from the SEM stations localised at the Wełna River (Oborniki and Rogoźno) (Fig. 1) and covered a period of 13 years (2005–2018). Three statistical measures, coefficient of determination (R2)43, percent bias (PBIAS)44, and Kling-Gupta efficiency (KGE)45, have been used to indicate the Wełna River model performance (Supplementary Tables S2 and S3). In terms of the quantitative component, the calibration and verification coefficients R2, KGE and PBIAS classified the model performance generally as good and very good for the main river (Wełna), and satisfactory and good for its tributary (Flinta). During the validation procedure, all coefficient values rated the model performance for daily flow simulations as very good. In terms of qualitative components, the model performance for TN simulations can be considered as very good or good, according to the all-applied coefficients. Lower model performance, mostly satisfactory, was observed for TP mainly due to the variability of phosphorus temporal distribution patterns (Supplementary Table S2). The entire process was described in detail in Orlińska-Woźniak et al46.Variant scenariosIn order to determine the contribution of individual sources to the total load of nutrients in the profile closing the analysed catchment, a final simulation of the model was used and subjected to calibration, verification and validation procedures, and called the baseline scenario (A0). Subsequent so-called variant scenarios (A1–A5), i.e. model simulations, were developed. In variant scenarios the values of selected parameters were changed in relation to the A0 scenario. This was used both in the river bed phase for point sources (A1) and for individual diffuse sources (A2–5), thus imitating surface changes for particular types of land use in the land phase of the catchment (Fig. 3).Figure 3Variant analysis diagram for assessment of nutrient loads (L) for particular modelling scenarios and sources described in the text: MWS, INS, SCS—point sources, URB—urban, AGS—agricultural, MFS—forest.Full size imageIn the A1 scenario, all parameterized and aggregated point sources (MWS, INS, SCS) for each relevant sub-basin (LMWS,INS,SCS), were removed from the model to calculate their contribution to the total nutrient loads in the closing profile of the studied catchment (LA1).In the next two scenarios (A2 and A3), concerning urban and agricultural land use, their surface areas (5 663 ha and 192 917 ha, respectively) were successively replaced by the forest land use. This procedure was based on the assumption that the forest is the primary type of land use for this catchment area47. In order to completely eliminate the influence of these areas, the nutrient loads from the relevant surface area occupied by forest land use were subtracted, in order to estimate the contribution of urban and agricultural land (LURB and LAGS, respectively).The change in land use from urbanised and agricultural areas to forest areas increased their percentage of the catchment area to almost 100%, thus the original image of the catchment area and the nutrient load at its mouth. On this basis, in scenario A4, the nutrient load from forests LMFS, which currently occupy only 20% of the catchment area (A0), flowing to the closing profile, was calculated from the proportion.The A5 scenario is the difference between the nutrient load from the A0 scenario and the sum of the remaining loads from the subsequent variant scenarios (A1–A4). In this way, both the natural background (NBS) and atmospheric deposition (ATS) were taken into account. More

Kilpatrick, A. M. et al. Lyme disease ecology in a changing world: consensus, uncertainty and critical gaps for improving control. Philos. Trans. R. Soc. B-Biol. Sci. 372, 15. https://doi.org/10.1098/rstb.2016.0117 (2017).Article 

Google Scholar 
Adenubi, O. T. et al. Pesticidal plants as a possible alternative to synthetic acaricides in tick control: A systematic review and meta-analysis. Ind. Crop. Prod. 123, 779–806. https://doi.org/10.1016/j.indcrop.2018.06.075 (2018).CAS 
Article 

Google Scholar 
Jordan, R. A. & Schulze, T. L. Availability and nature of commercial tick control services in three Lyme disease endemic states. J. Med. Entomol. 57, 807–814. https://doi.org/10.1093/jme/tjz215 (2019).CAS 
Article 

Google Scholar 
Isman, M. B. Botanical insecticides in the twenty-first century – Fulfilling their promise?. Ann. Rev. Entomol. 65, 233–249 (2020).CAS 
Article 

Google Scholar 
Eisen, L. Control of ixodid ticks and prevention of tick-borne diseases in the United States: The prospect of a new Lyme disease vaccine and the continuing problem with tick exposure on residential properties. Ticks Tick-Borne Dis. https://doi.org/10.1016/j.ttbdis.2021.101649 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Santos, A. C. C. et al. Apis mellifera (Insecta: Hymenoptera) in the target of neonicotinoids: A one-way ticket? Bioinsecticides can be an alternative. Ecotoxicol. Environ. Safe. 163, 28–36. https://doi.org/10.1016/j.ecoenv.2018.07.048 (2018).CAS 
Article 

Google Scholar 
Matos, W. B. et al. Potential source of ecofriendly insecticides: Essential oil induces avoidance and cause lower impairment on the activity of a stingless bee than organosynthetic insecticides, in laboratory. Ecotoxicol. Environ. Safe. 209, 111764. https://doi.org/10.1016/j.ecoenv.2020.111764 (2021).CAS 
Article 

Google Scholar 
Gashout, H. A., Guzman-Novoa, E., Goodwin, P. H. & Correa-Benítez, A. Impact of sublethal exposure to synthetic and natural acaricides on honey bee (Apis mellifera) memory and expression of genes related to memory. J. Insect Physiol. 121, 104014. https://doi.org/10.1016/j.jinsphys.2020.104014 (2020).CAS 
Article 
PubMed 

Google Scholar 
Eisen, L. & Dolan, M. C. Evidence for personal protective measures to reduce human contact with Blacklegged ticks and for environmentally based control methods to suppress host-seeking Blacklegged ticks and reduce infection with Lyme disease spirochetes in tick vectors and rodent reservoirs. J. Med. Entomol. 53, 1063–1092. https://doi.org/10.1093/jme/tjw103 (2016).Article 
PubMed 

Google Scholar 
Dyer, M. C., Requintina, M. D., Berger, K. A., Puggioni, G. & Mather, T. N. Evaluating the effects of minimal risk natural products for control of the tick, Ixodes scapularis (Acari: Ixodidae). J. Med. Entomol. 58, 390–397. https://doi.org/10.1093/jme/tjaa188 (2021).CAS 
Article 
PubMed 

Google Scholar 
Schulze, T. L. & Jordan, R. A. Synthetic pyrethroid, natural product, and entomopathogenic fungal acaricide product formulations for sustained early season suppression of host-seeking Ixodes scapularis (Acari: Ixodidae) and Amblyomma americanum nymphs. J. Med. Entomol. 58, 814–820. https://doi.org/10.1093/jme/tjaa248 (2021).CAS 
Article 
PubMed 

Google Scholar 
Bharadwaj, A., Stafford, K. C. & Behle, R. W. Efficacy and environmental persistence of nootkatone for the control of the Blacklegged tick (Acari: Ixodidae) in residential landscapes. J. Med. Entomol. 49, 1035–1044. https://doi.org/10.1603/me11251 (2012).Article 
PubMed 

Google Scholar 
Pavela, R. & Sedlák, P. Post-application temperature as a factor influencing the insecticidal activity of the essential oil from Thymus vulgaris. Ind. Crop. Prod. 113, 46–49 (2018).CAS 
Article 

Google Scholar 
Brunner, J. L., Killilea, M. & Ostfeld, R. S. Overwintering survival of nymphal Ixodes scapularis (Acari: Ixodidae) under natural conditions. J. Med. Entomol. 49, 981–987. https://doi.org/10.1603/me12060 (2012).Article 
PubMed 

Google Scholar 
Chown, S. L. & Nicolson, S. W. Insect Physiol. Ecol. (Oxford University Press, 2004).Ogden, N. H., Beard, C. B., Ginsberg, H. S. & Tsao, J. I. Possible effects of climate change on Ixodid ticks and the pathogens they transmit: Predictions and observations. J. Med. Entomol. 58, 1536–1545 (2021).Article 

Google Scholar 
Ballard, K. & Bone, C. Exploring spatially varying relationships between Lyme disease and land cover with geographically weighted regression. Appl. Geo. 127, 102383 (2021).Article 

Google Scholar 
Neelakanta, G., Sultana, H., Fish, D., Anderson, J. F. & Fikrig, E. Anaplasma phagocytophilum induces Ixodes scapularis ticks to express an antifreeze glycoprotein gene that enhances their survival in the cold. J. Clin. Invest. 120, 3179–3190. https://doi.org/10.1172/jci42868 (2010).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Adamo, S. A. Animals have a Plan B: how insects deal with the dual challenge of predators and pathogens. J. Comp. Physiol. B-Biochem. Syst. Environ. Physiol. 190, 381–390. https://doi.org/10.1007/s00360-020-01282-5 (2020).Article 

Google Scholar 
Adamo, S. A. How insects protect themselves against combined starvation and pathogen challenges, and the implications for reductionism. Comp. Biochem. Physiol. B-Biochem. Molec. Biol. https://doi.org/10.1016/j.cbpb.2021.110564 (2021).Article 

Google Scholar 
Linske, M. A. et al. Impacts of deciduous leaf litter and snow presence on nymphal Ixodes scapularis (Acari: Ixodidae) overwintering survival in coastal New England, USA. Insects https://doi.org/10.3390/insects10080227 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Burtis, J. C., Fahey, T. J. & Yavitt, J. B. Survival and energy use of Ixodes scapularis nymphs throughout their overwintering period. Parasitol. 146, 781–790. https://doi.org/10.1017/s0031182018002147 (2019).Article 

Google Scholar 
Boehnke, D., Gebhardt, R., Petney, T. & Norra, S. On the complexity of measuring forests microclimate and interpreting its relevance in habitat ecology: the example of Ixodes ricinus ticks. Parasit. Vectors 10, 549. https://doi.org/10.1186/s13071-017-2498-5 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Lindsay, L. R. et al. Survival and development of Ixodes scapularis (Acari, Ixodidae) under various climatic conditions in Ontario, Canada. J. Med. Entomol. 32, 143–152. https://doi.org/10.1093/jmedent/32.2.143 (1995).CAS 
Article 
PubMed 

Google Scholar 
Lindsay, L. R. et al. Survival and development of the different life stages of Ixodes scapularis (Acari: Ixodidae) held within four habitats on Long Point, Ontario, Canada. J. Med. Entomol. 35, 189–199. https://doi.org/10.1093/jmedent/35.3.189 (1998).CAS 
Article 
PubMed 

Google Scholar 
Ginsberg, H. S. et al. Woodland type and spatial distribution of nymphal Ixodes scapularis (Acari: Ixodidae). Environ. Entomol. 33, 1266–1273. https://doi.org/10.1603/0046-225x-33.5.1266 (2004).Article 

Google Scholar 
Clow, K. M. et al. The influence of abiotic and biotic factors on the invasion of Ixodes scapularis in Ontario, Canada. Ticks Tick-Borne Dis. 8, 554–563. https://doi.org/10.1016/j.ttbdis.2017.03.003 (2017).Article 
PubMed 

Google Scholar 
Natural Resources Canada. Balsam fir, (2015).Khatchikian, C. E. et al. Recent and rapid population growth and range expansion of the Lyme disease tick vector, Ixodes scapularis North America. Evolution 69, 1678–1689. https://doi.org/10.1111/evo.12690 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Pichette, A., Larouche, P. L., Lebrun, M. & Legault, J. Composition and antibacterial activity of Abies balsamea essential oil. Phytotherapy Res. 20, 371–373 (2006).CAS 
Article 

Google Scholar 
Poaty, B., Lahlah, J., Porqueres, F. & Bouafif, H. Composition, antimicrobial and antioxidant activities of seven essential oils from the North American boreal forest. World J. Microbiol. Biotechnol. 31, 907–919. https://doi.org/10.1007/s11274-015-1845-y (2015).CAS 
Article 
PubMed 

Google Scholar 
Beasley, T. M. & Schumacker, R. E. Multiple regression approach to analyzing contingency tables: Post hoc and planned comparison procedures. J. Exp. Ed. 64, 79–93. https://doi.org/10.1080/00220973.1995.9943797 (1995).Article 

Google Scholar 
Canon, L., Deslauriers, A., Mshvildadze, V. & Pichette, A. Volatile compounds in the foliage of balsam fir analyzed by static headspace gas chromotography (HS-GS): An example of the spruce budworm defoliation effect in the boreal forest of Quebec, Canada. Microchem. J. 110, 587–590 (2013).Article 

Google Scholar 
Faraone, N., MacPherson, S. & Hillier, N. K. Behavioral responses of Ixodes scapularis tick to natural products: development of novel repellents. Exp. Appl. Acarol. 79, 195–207. https://doi.org/10.1007/s10493-019-00421-0 (2019).CAS 
Article 
PubMed 

Google Scholar 
McMillan, L. E., Miller, D. W. & Adamo, S. A. Eating when ill is risky: immune defense impairs food detoxification in the caterpillar Manduca sexta. J. Exp. Biol. 221, 173336 (2018).
Google Scholar 
Gazave, E., Chevillon, C., Lenormand, T., Marquine, M. & Raymond, M. Dissecting the cost of insecticide resistance genes during the overwintering period of the mosquito Culex pipiens. Heredity 87, 441–448 (2001).CAS 
Article 

Google Scholar 
Lalouette, L., Williams, C. M., Hervant, F., Sinclair, B. J. & Renault, D. Metabolic rate and oxidative stress in insects exposed to low temperature thermal fluctuations. Comp. Biochem. Physiol. A 158, 229–234 (2011).CAS 
Article 

Google Scholar 
Clark, D. D. Lower temperature limits for activity of several Ixodid ticks: Effects of body size and rate of temperature change. J. Med. Entomol. 32, 449–452 (1995).CAS 
Article 

Google Scholar 
Carroll, J. F. & Kramer, M. Winter activity of Ixodes scapularis (Acari : Ixodidae) and the operation of deer-targeted tick control devices in Maryland. J. Med. Entomol. 40, 238–244. https://doi.org/10.1603/0022-2585-40.2.238 (2003).CAS 
Article 
PubMed 

Google Scholar 
Ginsberg, H. S. et al. Environmental factors affecting survival of immature Ixodes scapularis and implications for geographical distribution of Lyme disease: the climate/behavior hypothesis. PLoS ONE 12, e0168723. https://doi.org/10.1371/journal.pone.0168723 (2017).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Quadros, D. G., Johnson, T. L., Whitney, T. R., Oliver, J. D. & Chavez, A. S. O. Plant-derived natural compounds for tick pest control in livestock and wildlife: Pragmatism or utopia?. Insects https://doi.org/10.3390/insects11080490 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Ogendo, J. et al. Biocontrol potential of selected plant essential oil constituents as fumigants of insect pests attacking stored food commodities. Health 10, 287–318 (2011).
Google Scholar 
Panella, N. A., Karchesy, J., Maupin, G. O., Malan, J. C. & Piesman, J. Susceptibility of immature Ixodes scapularis (Acari: Ixodidae) to plant-derived acaricides. J. Med. Entomol. 34, 340–345 (1997).CAS 
Article 

Google Scholar 
Rosado-Aguilar, J. A. et al. Plant products and secondary metabolites with acaricide activity against ticks. Vet. Parasitol. 238, 66–76. https://doi.org/10.1016/j.vetpar.2017.03.023 (2017).CAS 
Article 
PubMed 

Google Scholar 
Jaenson, T. G. T., Carboui, S. & Palsson, K. Repellency of oils of lemon eucalyptus, geranium, and lavender and the mosquito repellent MyggA natural to Ixodes ricinus (Acari : Ixodidae) in the laboratory and field. J. Med. Entomol. 43, 731–736. https://doi.org/10.1603/0022-2585(2006)43[731:Rooole]2.0.Co;2 (2006).CAS 
Article 
PubMed 

Google Scholar 
Eigbrett, C. Natural Sourcing Organic Essential Oils Oxford, Connecticut, USA, .praannaturals.com/downloads/msds/SDS_Organic_Essential_Oil_Fir_Balsam_Canada.pdf (2016).Schulze, T. L. et al. Efficacy of granular deltamethrin against Ixodes scapularis and Amblyomma americanum (Acari: Ixodidae) nymphs. J. Med. Entomol. 38, 344–346. https://doi.org/10.1603/0022-2585-38.2.344 (2001).CAS 
Article 
PubMed 

Google Scholar 
Elias, S. P. et al. Effect of a botanical acaricide on Ixodes scapularis (Acari: Ixodidae) and nontarget arthropods. J. Med. Entomol. 50, 126–136. https://doi.org/10.1603/me12124 (2013).Article 
PubMed 

Google Scholar 
Burtis, J. C., Yavitt, J. B., Fahey, T. J. & Ostfeld, R. S. Ticks as soil-dwelling arthropods: an intersection between disease and soil ecology. J. Med. Entomol. 56, 1555–1564. https://doi.org/10.1093/jme/tjz116 (2019).Article 
PubMed 

Google Scholar 
Burtis, J. C., Ostfeld, R. S., Yavitt, J. B. & Fahey, T. J. The relationship between soil arthropods and the overwinter survival of Ixodes scapularis (Acari: Ixodidae) under manipulated snow cover. J. Med. Entomol. 53, 225–229. https://doi.org/10.1093/jme/tjv151 (2016).CAS 
Article 
PubMed 

Google Scholar 
Guerra, M. et al. Predicting the risk of Lyme disease: Habitat suitability for Ixodes scapularis in the north central United States. Emerg. Infect. Dis. 8, 289–297. https://doi.org/10.3201/eid0803.010166 (2002).Article 
PubMed 
PubMed Central 

Google Scholar 
Bunnell, J. E., Price, S. D., Das, A., Shields, T. M. & Glass, G. E. Geographic information systems and spatial analysis of adult Ixodes scapularis (Acari: Ixodidae) in the Middle Atlantic region of the USA. J. Med. Entomol. 40, 570–576. https://doi.org/10.1603/0022-2585-40.4.570 (2003).Article 
PubMed 

Google Scholar 
Lubelczyk, C. B. et al. Habitat associations of Ixodes scapularis (Acari: Ixodidae) in Maine. Environ. Entomol. 33, 900–906. https://doi.org/10.1603/0046-225x-33.4.900 (2004).Article 

Google Scholar 
Killilea, M. E., Swei, A., Lane, R. S., Briggs, C. J. & Ostfeld, R. S. Spatial dynamics of Lyme disease: A review. EcoHealth 5, 167–195. https://doi.org/10.1007/s10393-008-0171-3 (2008).Article 
PubMed 

Google Scholar 
Stafford, K. C. Survival of immature Ixodes scapularis (Acari: Ixodidae) at different relative humidities. J. Med. Entomol. 31, 310–314 (1994).Article 

Google Scholar 
Bertrand, M. R. & Wilson, M. L. Microclimate-dependent survival of unfed adult Ixodes scapularis (Acari: Ixodidae) in Nature: Life cycle and study design implications. J. Med. Entomol. 33, 619–627 (1996).CAS 
Article 

Google Scholar 
Lindsay, L. R. et al. Microclimate and habitat in relation to Ixodes scapularis (Acari: Ixodidae) populations on Long Point, Ontario, Canada. J. Med. Entomol. 36, 255–262. https://doi.org/10.1093/jmedent/36.3.255 (1999).CAS 
Article 
PubMed 

Google Scholar 
Thompson, C., Spielman, A. & Krause, P. J. Coinfecting deer-associated zoonoses: Lyme disease, babesiosis, and ehrlichiosis. Clin. Infect. Dis. 33, 676–685 (2001).CAS 
Article 

Google Scholar 
Hinckley, A. F. et al. effectiveness of residential acaricides to prevent Lyme and other tick-borne diseases in humans. J. Infect. Dis. 214, 182–188. https://doi.org/10.1093/infdis/jiv775 (2016).Article 
PubMed 

Google Scholar 
Keesing, F. et al. Effects of Ttck-control interventions on tick abundance, human encounters with Ttcks, and incidence of tickborne diseases in residential neighborhoods, New York, USA. Emerg. Infect. Dis. 28, 957–966. https://doi.org/10.3201/eid2805.211146 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Hayes, L. E., Scott, J. A. & Stafford, K. C. Influences of weather on Ixodes scapularis nymphal densities at long-term study sites in Connecticut. Ticks Tick-Borne Dis. 6, 258–266. https://doi.org/10.1016/j.ttbdiS.2015.01.006 (2015).Article 
PubMed 

Google Scholar 
Rand, P. W. et al. Trial of a minimal-risk botanical compound to control the vector tick of Lyme disease. J. Med. Entomol. 47, 695–698 (2010).CAS 
Article 

Google Scholar 
United Nations. Convention on Biological Diversity. (1992).Convention on International Trade in Endangered Species of Wild Fauna and Flora. (1973).Burtis, J. C. Method for the efficient deployment and recovery of Ixodes scapularis (Acari: Ixodidae) nymphs and engorged larvae from field microcosms. J. Med. Entomol. 54, 1778–1782. https://doi.org/10.1093/jme/tjx157 (2017).Article 
PubMed 

Google Scholar 
Nova Scotia Department of Natural Resources and Renewables Trees of the Acadian Forest (2021). More

Kyoto University microbiome researcher Hiroyuki Ogata says that the recent work2,3 further connects RNA viruses and the carbon pump, which affects the Earth’s biogeochemical cycles and thus its climate. And it sheds light on the diversity, evolution and ecology of RNA viruses, which has not previously been possible through applying the techniques of traditional DNA-based metagenomics. The team found many new lineages at the phylum-level by using “highly sensitive” computational approaches.It’s possible to assess the ecosystem impact of viruses by inferring auxiliary metabolic genes (AMGs). AMGs hint at the ways RNA viruses manipulate the physiology of their hosts as they seek to maximize production of more virus through the host. As Jian explains, labs have identified a variety of AMGs that are encoded by DNA viruses and, he says, it’s “well-recognized” that AMGs probably play a role in marine ecosystems. It was unknown if AMGs could be found in RNA viruses, which the recent Science paper2 has now established, he says. Jian sees this work as providing “a very important foundational dataset” for exploring questions connected to AMGs. “In my opinion, if more long-sequence or complete marine RNA virus genomes can be obtained in the future, and they can be further connected with specific hosts, it will greatly promote the understanding of the ecological impact of RNA viruses in the oceans.”To tease out AMGs, the scientists used a variety of tools, such as viral identification software for both DNA and RNA viruses, says Wainaina. The ones for DNA viruses are available on Cyverse, and the protocols for the tools from the Sullivan lab are on protocols.io. One method for RNA viruses is in progress and will be soon available on Cyverse, he says. DNA viral identification tools include VirSorter2, a pipeline for identifying viral sequence from metagenomics data, and the protocol for using this and other tools are also on protocols.io. To identify AMGs from viral sequence that had been identified through VirSorter, the team used use DRAM-v, a software tool from the lab of microbiome researcher Kelly Wrighton at Colorado State University. Her group had created Distilled and Refined Annotation of Metabolism (DRAM), a framework to resolve metabolic information from microbial data. The companion tool DRAM-v is for viruses and can be applied to metagenomic data sets for annotating metagenomics-based assembled genomes, for example through the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, and to contiguous viral sequences identified by VirSorter.The hunt for AMGs is one instance in which the team needed to determine in each case whether a sequence was likely ‘stolen’ from host cells, says Dominguez-Huerta. RNA viral genomes are less than 40 kilobases long and usually have complicated genomic organization, both in a structural genomics sense related to the physical arrangement of genes along the viral genome and in a functional sense in terms of transcription and translation: there are overlapping genes, frameshifts and more, all of which makes this kind of annotation difficult. And sometimes information in the annotation databases is wrong and indicates that a match is cellular when it is in fact viral. Thus, to find AMGs, “we don’t have a defined clean methodology automated in a pipeline yet,” he says. It remains a time-consuming task. Assigning putative function to the protein sequences encoded by AMGs also involves checking the literature and comparing different annotation sources.Dominguez-Huerta says he and the team were glad they could assemble AMG functionalities to suggest the range of ways in which RNA viruses manipulate the metabolisms of their hosts—from photosynthesis to central carbon metabolism to vacuolar digestion and RNA repair. This overview let them see how some AMGs are repeated across different viruses across the oceans. Finding AMGs in long-read sequence is what he calls a “fire test” for the lab. To avoid ‘false AMGs’ from unreliable matches, they use BLASTP, the Basic Alignment Search Tool that compares a protein query sequence to a protein database.“I am fascinated by the ability of viruses to metabolic reprogram not only their hosts but more importantly at the ecosystem level,” says Wainaina. It is probable that the AMGs the team identified “are a central cog in microbial metabolism networks.” Current and future modeling efforts will hopefully provide insights into the ecosystem roles of viruses—both DNA viruses and RNA viruses—and on a global scale both within the ocean ecosystem and beyond.Host inference is challenging, says Dominguez-Huerta, because, for example, viruses with RNA genomes do not share genetic information with their host genomic DNA the way dsDNA viruses do when they infect bacteria. That means there is no clear signal to be derived from the host genome to help one guess the possible host. But sometimes RNA viruses do integrate into host genomes, and those, likely more accidental, events were sufficient for the scientists to capture some signal to infer hosts. “We also performed statistical co-occurrence analytics using abundances to infer the hosts with certain success,” he says.Unlike dsDNA viruses, RNA viruses infect mostly eukaryotes, from protists and fungi to invertebrates and fish larvae; only a minority infect bacteria. Overall, the team has been able to capture “a picture of dsDNA viruses infecting prokaryotes and RNA viruses infecting eukaryotes in the oceans, complementing each other in their marine hosts,” says Dominguez-Huerta. The fact that the scientists can infer “that RNA viruses can steal genes from the host,” in the form of AMGs, to then reprogram host metabolism matters not only as scientists complete the picture of how viruses directly tune the activity of hosts during infection, but also in regard to how this influences biogeochemical cycles, he says. “We think that these AMGs are incorporated into the RNA virus genomes from cellular mRNA transcripts by non-homologous recombination,” he says. This gives, in his view, a new picture of RNA viruses, which, despite their small genome sizes, can squeeze in protein-coding genes. Such proteins could be sufficient to boost the production of virus particles per infected cell, perhaps increasing viral fitness in the difficult conditions of the oligotrophic open ocean and letting the viruses better propagate in the environment.More generally, says Dominguez-Huerta, capturing RNA from ocean samples is difficult, because RNA is physically fragile and degrades rapidly. When digging into metatranscriptomic data, which include the RNA from plankton and RNA from other organisms, less than 1% of this RNA is likely to be viral RNA, he says. Previously, some labs have first purified RNA from samples, enriched it for replicating RNA viruses and then applied a method called dsRNA-seq to recover dsRNA virus sequence and replicate sequences from single-stranded RNA viruses. For future ocean RNA virus projects, he says that the lab is currently working on a wet-lab method to purify RNA virus particles from seawater to solve the challenges of obtaining viral RNA for analysis. More

Microbial biodiversity surveys have often been done in a number of generally better-studied regions3, as with the San Pedro Time Series from the San Pedro Channel off the coast of Southern California. Global surveys have also been emerging, such as the Sorcerer II Global Ocean Sampling Expedition from 2004 to 2006 launched by J. Craig Venter. There are also data and samples from the Malaspina circumnavigation, an expedition devoted to data collection on ocean biodiversity and climate change that was led by the Spanish Ministry of Science and Innovation.As microbiome researcher Shinichi Sunagawa of the ETH Zurich and colleagues point out4, sequencing technologies have advanced such that they now enable systematic and quantitative global ocean surveys. These advances, in turn, made it possible to find and assess marine double-stranded DNA virus populations. This latest work on marine RNA viruses, says Sunagawa, in which he was also involved, embeds new phylum-level findings into a “robust taxonomic framework.” In his view, this research ranks in importance with the reconstruction a few years ago of a group of bacterial genomes representing more than 35 phyla that the researchers call “the candidate phyla radiation”5. If one counts viruses in with other taxonomic groups, the finding might be the largest single expansion of established microbial taxonomy, he says. And he especially likes the definition of a new basal Orthornavirae megataxon, the proposed phylum ‘Taraviricota’. This proposed phylum is one of several findings from recently published analyses of sampling data from Tara Oceans1,2, a global expedition supported by the Tara Ocean Foundation, or Fondation Tara Océan, based in France and with many partner organizations and supporters. The foundation is a major source of global data about the ocean and ocean microbes and, as its president Étienne Bourgois says, it’s a “family project.” The family business is the French fashion house agnès b., founded by his mother Agnès Troublé.Because the family cares about the sea, they bought a 36-meter schooner from Lady Pippa Blake, widow of yachtsman and explorer Sir Peter Blake, after pirates killed him during an environmental expedition in the Amazon delta, and turned it into the expedition vessel and floating science laboratory Tara, devoted to understanding and protecting the world’s marine environment. It’s a way to continue what Peter Blake started, to continue the conversation about the ocean and do research as well, says sailor-scientist Romain Troublé, executive director of the foundation and nephew of Agnès Troublé. The boat had been previously owned by explorer Jean-Louis Étienne. The foundation has supported several expeditions with Tara including the Tara Oceans and Tara Oceans Polar Circle expeditions, as well as Tara Mission Microbiomes, which is currently underway. The equilibrium of the planet “depends on the microbiome of the ocean in the same way we depend on our own microbiome,” says Romain Troublé. Viruses are part of the larger picture of how life is supported on the planet. It’s “a great mystery of the century” to decipher the roles, behaviors and functions of the ocean microbiome, including its beneficial effects. Over the last decade, he says, the expeditions have, for example, collected plankton samples from coastal waters, coral reefs and the high seas around the world for scientists to ask questions of. Microplastics in the ocean concentrate chemical pollutants such as pesticides, and microplastics appear to be substrates for distinct microbiomes. Polystyrene and polypropylene, for example, harbor different microbial communities. “We call it the plastisphere,” he says. All sample collection, not just of microplastics, happens with a view to scientific rigor to assure data quality, says Troublé. Many institutes are part of and support the expeditions through the Tara Ocean Foundation, including AtlantECO, the French Ministry of Research, the Swiss National Science Foundation, the US National Science Foundation, the European Molecular Biology Laboratory and the French National Centre for Scientific Research.Tara Oceans was an expedition initiated by EMBL researcher Eric Karsenti, here in the foreground. He is checking a rosette of Niskin bottles that collect water, and ocean microbe samples, at various depths. Sensors capture parameters such as temperature.
Credit: Fondation Tara OcéanIts expedition Tara Oceans was initiated by cell and marine biologist Eric Karsenti of the European Molecular Biology Laboratory. The expedition ran from 2009 to 2013 and covered 125,000 kilometers of ocean, taking ocean water and samples. It collected nearly 35,000 samples of viruses, algae and plankton and delivered more than 60 terabases of DNA and RNA sequences.The research community strives to follow FAIR data principles, the principles of findability, accessibility, interoperability and reusability, says Sunagawa. Tara Ocean’s data troves can be found, for instance, in the European Nucleotide Archive (ENA), Pangeaea, Cyverse, iVIRUS and on Genoscope. Other data-collection efforts target users with less programming experience and offer various types of data relevant to marine microbial research, he says: for example, the Ocean Gene Atlas, a portal to search for a gene or protein sequence to see, for instance, its abundance on an ocean map. The Ocean Barcode Atlas lets users explore, for example, operational taxonomic units (OTU) data and plankton communities from Tara Oceans and OTUs from Malaspina prokaryote data. Sunagawa also points to the Ocean Microbiomics Database and its high-quality genome-resolved information about the global microbiome, which has sequencing data from 2003 onwards and which includes Tara Oceans data as well as datasets such as the Hawaii Ocean Time-Series (HOT), the Bermuda Atlantic Time-series Study (BATS), with its collection of ocean data dating back to 1988, and BioGeotraces, with hydrographic and marine geochemical data from various expeditions.The recent publications on RNA viruses1,2, in which Sunagawa was also involved, have expanded the known diversity of these viruses, he says. They build on efforts by, for example, the research team that created and applied a cloud-based infrastructure called Serratus6, with which researchers can perform sequence alignment using bowtie2 for nucleotide sequences and DIAMOND2 for protein sequences in ‘ultra-high throughput’ on a petabase scale. Using Serratus, the team identified more than 130,000 previously unknown RNA viruses, both on land and in the oceans. The wealth of resources for microbial and viral data about the oceans is helpful to the research community, but “we could still improve the connectivity between various datasets though,” says Sunagawa. That would help, for example, with searching and finding data products that are derived from primary data, such as identifiers of individual genome assemblies, genes and metagenome assembled genomes, which are all presented in different online locations. But connecting data resources is a project that itself takes resources, and such projects are hard to get funding for.Going forward, it will be challenging, says Sunagawa, to update and keep up to date both past projects and ongoing projects such as the Global Ocean Ship-based Hydrographic Investigations program (GO-SHIP), which is focused on physical oceanography; the Antarctic Circumnavigation Expedition (ACE), on carbon-cycle marine biogeochemistry; Mission Microbiomes; and many more. “And ultimately, we will need to cross boundaries that currently separate biome-focused research to better understand processes at the sea–land–atmosphere interfaces.”Tara Mission Microbiomes has been underway for nearly two years and wraps up in October 2022. At press time, the schooner Tara was off the Angolan Coast. At the end of the expedition, it will have traveled a total of 70,000 km of ocean area around South America, Africa, Europe and Antarctica. Mission Microbiomes is part of the EU-funded AtlantECO and also includes 42 research organizations from 13 countries. The microbiome mission is collecting data on how climate change is affecting the marine microbiome, on how pollution, microplastics pollution in particular, affects the marine environments and on the beneficial impact of the ocean microbiome.Krill are small ocean crustaceans that mainly eat phytoplankton and are a food source for animals such as whales and seals. Krill play a crucial role in biogeochemical cycles.
Credit: F. Aurat, Fondation Tara OcéanChris Bowler, from the Institut de Biologie de l’École Normale Supérieure, is scientific director of the Tara Oceans consortium, was scientific coordinator of the Tara Oceans expedition and was onboard in Antarctica during the Tara Mission Microbiomes expedition to collect data on the impact of icebergs on the Weddell Sea ecosystem. The project’s scientists in Tara Mission Microbiomes, he says, are studying specific processes, including the Amazon plume, the Malvinas confluence, the impact of tabular icebergs in the Weddell Sea, the Benguela upwelling and more. The data from this expedition will be similar to those from Tara Oceans but, he says, “we will have much more contextual data related to the specific processes we have been studying.” The applied techniques are all ones that have undergone much advancement since Tara Oceans, he says. They include long-read sequencing, Hi-C sequencing to capture chromatin organization on a genome-wide basis and various types of microscopy.Data and results from previous and ongoing expeditions are impressive, says Sunagawa but “we are still data-limited in our field of research.” Geographically, sampling stations are usually still separated by hundreds of kilometers, and often they are even further apart than that. This means that what is missing is both temporal and seasonal resolution, “and we keep detecting new organisms,” he says. Tara Mission Microbiomes will help to fill in some of these gaps. The mission is unlike Tara Oceans, with its focus more on coastal areas and environmental pollutants such as microplastics. Sunagawa and his group are not currently involved with Tara Mission Microbiomes, “but we look forward to seeing the first results coming out soon.”Through photosynthesis, phytoplankton deliver oxygen to the planet. They are food for zooplankton, which are food for other marine organisms. This food web and its associated decomposition are part of the ocean’s carbon pump, in which marine viruses play an important role that scientists have only begun exploring.
Credit: M. Bardy, Fondation Tara Océan More