Ecology

Boyle, T. H. & Anderson, E. in Cacti: Biology and Uses (ed. Nobel, P. S.) 125–141 (Univ. California Press, 2002).Gibson, A. C. & Nobel, P. S. The Cactus Primer (Harvard Univ. Press, 1986).Bravo Hollis, H. & Sánchez Mejorada, H. Las Cactáceas de México (Univ. Nacional Autónoma de México, 1978).Goettsch, B. et al. High proportion of cactus species threatened with extinction. Nat. Plants 1, 15142 (2015).CAS 
PubMed 

Google Scholar 
Benavides, E., Breceda, A. & Anadón, J. D. Winners and losers in the predicted impact of climate change on cacti species in Baja California. Plant Ecol. 222, 29–44 (2021).
Google Scholar 
Nobel, P. S. Responses of some North American CAM plants to freezing temperatures and doubled CO2 concentrations: implications of global climate change for extending cultivation. J. Arid. Environ. 34, 187–196 (1996).
Google Scholar 
Reyes-García, C. & Andrade, J. L. Crassulacean acid metabolism under global climate change. N. Phytol. 181, 754–757 (2009).
Google Scholar 
Smith, S. D., Didden-Zopfy, B. & Nobel, P. S. High-temperature responses of North American cacti. Ecology 65, 643–651 (1984).
Google Scholar 
Larios, E., González, E. J., Rosen, P. C., Pate, A. & Holm, P. Population projections of an endangered cactus suggest little impact of climate change. Oecologia 192, 439–448 (2020).PubMed 

Google Scholar 
Esparza-Olguı́n, L., Valverde, T. & Vilchis-Anaya, E. Demographic analysis of a rare columnar cactus (Neobuxbaumia macrocephala) in the Tehuacan Valley, Mexico. Biol. Conserv. 103, 349–359 (2002).
Google Scholar 
Seal, C. E. et al. Thermal buffering capacity of the germination phenotype across the environmental envelope of the Cactaceae. Glob. Change Biol. 23, 5309–5317 (2017).
Google Scholar 
Huang, J., Yu, H., Guan, X., Wang, G. & Guo, R. Accelerated dryland expansion under climate change. Nat. Clim. Change 6, 166–171 (2016).
Google Scholar 
Gurvich, D. E. et al. Combined effect of water potential and temperature on seed germination and seedling development of cacti from a mesic Argentine ecosystem. Flora 227, 18–24 (2017).
Google Scholar 
Nuzhyna, N., Baglay, K., Golubenko, A. & Lushchak, O. Anatomically distinct representatives of Cactaceae Juss. family have different response to acute heat shock stress. Flora 242, 137–145 (2018).
Google Scholar 
Andrade, J. L. & Nobel, P. S. Microhabitats and water relations of epiphytic cacti and ferns in a lowland neotropical forest. Biotropica 29, 261–270 (1997).
Google Scholar 
Williams, D. G., Hultine, K. R. & Dettman, D. L. Functional trade-offs in succulent stems predict responses to climate change in columnar cacti. J. Exp. Bot. 65, 3405–3413 (2014).PubMed 

Google Scholar 
Aragón-Gastélum, J. L. et al. Induced climate change impairs photosynthetic performance in Echinocactus platyacanthus, an especially protected Mexican cactus species. Flora Morphol. Distrib. Funct. Ecol. Plants 209, 499–503 (2014).
Google Scholar 
Martorell, C., Montañana, D. M., Ureta, C. & Mandujano, M. C. Assessing the importance of multiple threats to an endangered globose cactus in Mexico: cattle grazing, looting and climate change. Biol. Conserv. 181, 73–81 (2015).
Google Scholar 
Dávila, P., Téllez, O. & Lira, R. Impact of climate change on the distribution of populations of an endemic Mexican columnar cactus in the Tehuacán-Cuicatlán Valley, Mexico. Plant Biosyst. 147, 376–386 (2013).
Google Scholar 
Conver, J. L., Foley, T., Winkler, D. E. & Swann, D. E. Demographic changes over >70 yr in a population of saguaro cacti (Carnegiea gigantea) in the northern Sonoran Desert. J. Arid. Environ. 139, 41–48 (2017).
Google Scholar 
Carrillo-Angeles, I. G., Suzán-Azpiri, H., Mandujano, M. C., Golubov, J. & Martínez-Ávalos, J. G. Niche breadth and the implications of climate change in the conservation of the genus Astrophytum (Cactaceae). J. Arid. Environ. 124, 310–317 (2016).
Google Scholar 
de Cavalcante, A. M. B. & de Duarte, A. S. Modeling the distribution of three cactus species of the Caatinga biome in future climate scenarios. Int. J. Ecol. Environ. Sci. 45, 191–203 (2019).
Google Scholar 
de Cavalcante, A. M. B., de Duarte, A. S. & Ometto, J. P. H. B. Modeling the potential distribution of Epiphyllum phyllanthus (L.) Haw. under future climate scenarios in the Caatinga biome. An. Acad. Bras. Cienc. 92, 351–358 (2020).
Google Scholar 
Tellez-Valdes, O. & DiVila-Aranda, P. Protected areas and climate change: a case study of the cacti in the Tehuacan-Cuicatlan biosphere reserve, Mexico. Conserv. Biol. 17, 846–853 (2003).
Google Scholar 
dos Santos Simões, S., Zappi, D., da Costa, G. M., de Oliveira, G. & Aona, L. Y. S. Spatial niche modelling of five endemic cacti from the Brazilian Caatinga: past, present and future. Austral Ecol. 45, 1–13 (2019).
Google Scholar 
Gorostiague, P., Sajama, J. & Ortega-Baes, P. Will climate change cause spatial mismatch between plants and their pollinators? A test using Andean cactus species. Biol. Conserv. 226, 247–255 (2018).
Google Scholar 
Butler, C. J., Wheeler, E. A. & Stabler, L. B. Distribution of the threatened lace hedgehog cactus (Echinocereus reichenbachii) under various climate change scenarios. J. Torre. Bot. Soc. 139, 46–55 (2012).
Google Scholar 
Johnson, C. N. Species extinction and the relationship between distribution and abundance. Nature 394, 272–274 (1998).CAS 

Google Scholar 
Thuiller, W., Lavorel, S. & Araújo, M. B. Niche properties and geographical extent as predictors of species sensitivity to climate change. Glob. Ecol. Biogeogr. 14, 347–357 (2005).
Google Scholar 
Enquist, B. J. Cyberinfrastructure for an integrated botanical information network to investigate the ecological impacts of global climate change on plant biodiversity. Preprint at PeerJ https://doi.org/10.7287/peerj.preprints.2615v2 (2016).Buisson, L., Thuiller, W., Casajus, N., Lek, S. & Grenouillet, G. Uncertainty in ensemble forecasting of species distribution. Glob. Change Biol. 16, 1145–1157 (2010).
Google Scholar 
Thuiller, W., Guéguen, M., Renaud, J., Karger, D. N. & Zimmermann, N. E. Uncertainty in ensembles of global biodiversity scenarios. Nat. Commun. 10, 1446 (2019).PubMed 
PubMed Central 

Google Scholar 
Goettsch, B., Durán, A. P. & Gaston, K. J. Global gap analysis of cactus species and priority sites for their conservation. Conserv. Biol. 33, 369–376 (2018).PubMed 

Google Scholar 
Maitner, B. S. et al. The bien R package: A tool to access the Botanical Information and Ecology Network (BIEN) database. Methods Ecol. Evol. 9, 373–379 (2018).
Google Scholar 
Karger, D. N. et al. Climatologies at high resolution for the Earth’s land surface areas. Sci. Data 4, 170122 (2017).PubMed 
PubMed Central 

Google Scholar 
Sanderson, B. M., Knutti, R. & Caldwell, P. A representative democracy to reduce interdependency in a multimodel ensemble. J. Clim. 28, 5171–5194 (2015).
Google Scholar 
Brodzik, M. J., Billingsley, B., Haran, T., Raup, B. & Savoie, M. H. EASE-Grid 2.0: Incremental but significant improvements for Earth-gridded data sets. ISPRS Int. J. Geo-Inf. 1, 32–45 (2012).
Google Scholar 
Venter, O. et al. Global terrestrial human footprint maps for 1993 and 2009. Sci. Data 3, 160067 (2016).PubMed 
PubMed Central 

Google Scholar 
Phillips, S. maxnet: Fitting ‘maxent’ species distribution models with ‘glmnet’. R package version 0.1.4. https://CRAN.R-project.org/package=maxnet (2017).Friedman, J., Hastie, T. & Tibshirani, R. Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw. 33, 1–22 (2010).PubMed 
PubMed Central 

Google Scholar 
Dormann, C. F. et al. Collinearity: a review of methods to deal with it and a simulation study evaluating their performance. Ecography 36, 27–46 (2013).
Google Scholar 
Franklin, S. B., Gibson, D. J., Robertson, P. A., Pohlmann, J. T. & Fralish, J. S. Parallel analysis: a method for determining significant principal components. J. Veg. Sci. 6, 99–106 (1995).
Google Scholar 
Roberts, D. R. et al. Cross-validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure. Ecography 40, 913–929 (2017).
Google Scholar 
Merow, C., Smith, M. J. & Silander, J. A. A practical guide to MaxEnt for modeling species’ distributions: what it does, and why inputs and settings matter. Ecography 36, 1058–1069 (2013).
Google Scholar 
Allouche, O., Tsoar, A. & Kadmon, R. Assessing the accuracy of species distribution models: prevalence, kappa and the true skill statistic (TSS). J. Appl. Ecol. 43, 1223–1232 (2006).
Google Scholar 
Calabrese, J. M., Certain, G., Kraan, C. & Dormann, C. F. Stacking species distribution models and adjusting bias by linking them to macroecological models. Glob. Ecol. Biogeogr. 23, 99–112 (2014).
Google Scholar 
R Core Team R: A Language and Environment for Statistical Computing Version 3.6.0 (R Foundation for Statistical Computing, 2019). https://www.R-project.org/ More

Systematic palaeontology
Tetrapoda Jaekel, 1909 fide Sues20
Family undesignated
Termonerpeton makrydactylus gen. et sp. nov. (Fig. 1)Fig. 1: Termonerpeton makrydactylus gen. et sp. nov. holotype UMZC 2019.1.a Specimen photograph. b Interpretive drawing. Scale bars 10 mm. Abbreviations: acet acetabulum, fem femur, fib fibula, ha haemal arch, ic intercentrum, l left, na neural arch, phal phalanx, piliac p post-iliac process, plc pleurocentrum, r right, sac rib sacral rib, tib tibia.Full size image

EtymologyGenus: from τέρμωυ (térmon) meaning boundary and ερπετό (erpetó) meaning ‘crawler’, referring to the field boundary walls near the East Kirkton quarry where the late Stan Wood initially discovered fossils from the East Kirkton Limestone and from where the type specimen may have been collected; species: from μακρύς (makrýs) meaning ‘elongate’ and δάχτυλο (dáchtylo; more precisely, δάχτυλο ποδιού, dáchtylo podioú) meaning ‘toe’, referring to the very long pedal digit IV.HolotypeUniversity of Cambridge Museum of Zoology (UMZC) 2019.1. A partial tetrapod postcranium, preserving both pelves, a femur, fibula, tibia, and an almost complete but disarticulated pes. Closely associated with the appendicular elements are dorsally open hoop-shaped centra, a few neural and haemal arches, curved ribs, and a section of articulated gastralia.Locality and horizonEast Kirkton quarry, near Bathgate, Scotland, UK. East Kirkton Limestone, Bathgate Hills Volcanic Formation. Exact horizon is unknown. Brigantian, Viséan, early Carboniferous (=Mississippian)21.Differential diagnosisPossible autapomorphies: ilium with drawn-out, flat, blade-like dorsal process; very large, stout, and elongate metatarsal IV, greatly exceeding the length of metatarsals III and V (~30% or more). Possible tetrapod synapomorphies among post-Devonian taxa: distinct interepipodial space between tibia and fibula; well-ossified tarsus comprising tibiale, fibulare, intermedium, four centralia, and five distal tarsals. Possible amniote synapomorphies, but often showing reversed polarity in several stem- and crown amniote taxa: presumed pedal phalangeal formula 23454; robust and long pedal digit IV; enlarged intermedium and fibulare, together occupying more than half of proximal moiety of tarsus; curved ribs. Characters of uncertain polarity (also present in Caerorhachis): elongate, slender, and posterodorsally oblique post-iliac process; short puboischiadic plate with almost vertical anterior margin; stout femur with poorly pronounced waisting along the shaft, longer than puboischiadic plate; hoop-shaped centra.Attributed specimenNational Museums Scotland (NMS) G.1992.22.1. An articulated, partially complete, large tetrapod pes, preserving a nearly complete array of tarsals, all metatarsals, and the proximal phalanges of digits I–III. Unit 82, East Kirkton Limestone, East Kirkton quarry, near Bathgate, Scotland, UK.
Specimen description
Appendicular skeletonMost of the description is based upon the holotype. Both pelves are preserved, one mainly as a natural mould. The puboichiadic plates are short and deep, with an almost vertical anterior margin to the pubis (Fig. 1). In one, the surface of the puboischiadic plate is strongly convex, in the other it is strongly concave. The concave plate may belong to the left pelvis, with the concavity indicating the acetabulum. Both iliac processes of the presumed right ilium are overlain by a neural arch and part of the femur and cannot be seen. The presumed left ilium shows a long, posteriorly pointing post-iliac process that extends as far backward as the posterior edge of the ischium. It retains the proximal, stump-like portion of a dorsal iliac process, continued distally in natural mould as a mediolaterally flattened and blade-like structure. Both processes sit above a short iliac neck. The dorsal iliac process is proportionally longer than in other tetrapods and its knife-like appearance is unique. The angle between the two processes is much more acute than in most other tetrapods, and the nearest comparison is with the divided iliac process of the microsaurs Tuditanus and Ricnodon22 which, however, could merely represent a bifid post-iliac process. Two gaps in ossification are taken as evidence of an ilio-ischiadic suture half-way down the posterior margin on the left pelvis and an ilio-pubic suture halfway down the anterior margin of the right pelvis (Fig. 1). There is no evidence of a puboischiadic suture, although a shallow depression along the ventral margin of the left puboischiadic plate probably marks the junction between pubis and ischium. The complete left puboischiadic plate is 20 mm deep behind the ilium and 30 mm long, with the pubis contributing about one-third of its length and the ischium the remaining two thirds. The anterior margin of the pubis is almost vertical. The dorsal margin of the ischium is shallowly convex for half its length before extending posteroventrally to meet the upturned posterior extremity of the ischium’s ventral margin. There is no evidence as to the angle at which the two pelvic plates met at the symphysis, which would affect the position of the acetabulum relative to the substrate, and thus the effective resting posture of the hindlimb.The left femur is at least 39 mm in length, and longer than the puboischiadic plate. The entire bone is crushed, and its distal end lies partly beneath one of the pelvic halves and a neural arch so that its features cannot easily be made out. A possible intercondylar groove may be present distally, and the extensor surface of its proximal extremity appears to show a subcentral depression. The femur itself is robust with little waisting at mid-shaft. A small internal trochanter lies near its proximal end. The left fibula is approximately 26 mm long along its lateral margin. Its proximal end is narrow and grooved. Its broad and strongly flared distal end suggests a broad contact with the tarsus. The medial turn of the distal end indicates a large interepipodial space. The left tibia is about 20 mm long, slender, and shallowly waisted at mid-shaft. It is not clear which end is proximal and which distal, although probably the proximal is the broader. The tibia is probably more than half the length of the femur. Based upon the femur and tibia lengths, and omitting the ankle and pes, the above figures indicate a total stylopod-zeugopod length of about 65 mm, assuming a fully extended limb.Most of the morphology of the left pes is preserved, showing many well-ossified tarsal bones (Fig. 2). Several of these, including possible distal tarsals II and III lie more or less in anatomical continuity relative to metatarsals II and III, respectively. Other tarsal elements, including possible fibulare, tibiale, centralia, and distal tarsals, are illustrated in Fig. 2. Metatarsal IV lies in anatomical position relative to metatarsals II and III and, at 7 mm in length, it is significantly larger than the latter. The presumed first phalanx of pedal digit IV lies close to metatarsal IV, at an angle of nearly 90° to the latter. It is long and slender, indicating an unusually elongate fourth pedal digit.Fig. 2: Termonerpeton makrydactylus gen. et sp. nov. left hindlimb of UMZC 2019.1.a Specimen photograph, showing close-up view of hindlimb skeleton, b Interpretive drawing, with centralia, distal tarsals, and metatarsals indicated by red, blue, and black Roman numerals, respectively, c Interpretive drawing with dashed lines connecting elements of individual digits, d Reconstruction of left tibia, fibula and pes. Scale bars 10 mm. Abbreviations: interm intermedium, tib tibialia.Full size imageAn array of about 12 phalanges is preserved. They are all disrupted but occur in proximity to one another and, like the first phalanx of pedal digit IV, also mainly lie at right angles to metatarsals III and IV. An additional, acutely angled pointed ungual phalanx, possibly associated with digit II, is also visible. A further two phalanges have been displaced and rest along the anterior edge of the left pelvis. In total, we were, therefore, able to identify 15 elements. The preservation of the pes suggests it was strongly flexed either at death or from tissue shrinkage thereafter. An isolated metatarsal, presumably from the other, missing foot, lies some distance away near the edge of the block. Together, the pedal elements suggest a relatively large foot.A second specimen, NMS G.1992.22.1 (Fig. 3), is represented by an isolated pes. It may belong to Termonerpeton, although it is from a much larger individual. It shows five metatarsals of which the fourth is much longer and more robust than the other four and about twice as long as that of the holotype, while metatarsal V is the smallest. There are three phalanges, plus five distal tarsals. A D-shaped element closely associated with three centralia could be either a fibulare, a displaced intermedium, or centrale IV.Fig. 3: Termonerpeton makrydactylus gen. et sp. nov partial pes, attributed specimen NMS G.1992.22.1.a Specimen photograph, b with centralia, distal tarsals, and metatarsals indicated by red, blue, and black Roman numerals, respectively. Scale bars 10 mm.Full size imageAxial skeletonWhere visible, neural arches have short neural spines and prominent zygapophyses, but their shape is hard to assess as none is well preserved. The element overlying part of the right pelvis and the femur is 7 mm high in total. Numerous dorsally open, hoop-shaped centra about 5 mm in diameter are visible, as well as a few small, oval, shallowly curved elements (Fig. 1). Without further evidence, it is uncertain which of these elements are intercentra and which pleurocentra, though we assume that the larger elements are pleurocentra. The preserved ribs are slender and curved, and include trunk ribs, a possible presacral rib, a possible sacral rib, and a possible postsacral rib. This is long but more or less straight. A bone situated among a cluster of centra, somewhat distant from the other tarsal bones, was originally interpreted by us as a possible fibulare, similar to the fibulare in Proterogyrinus23. However, it might also be interpreted as a sacral rib. If so, its morphology is unique. It is short and widens distally into a fan-shaped structure but does not appear to have a bifid proximal end, unlike the sacral rib in Proterogyrinus23. Three haemal arches are present, one still attached to its half-hoop centrum, a second slightly longer, and a third very short and presumably from a more posterior region of the tail.ComparisonsThe exceptional preservation of tetrapods from the East Kirkton Limestone provides a unique opportunity to study portions of the skeletal anatomy that are otherwise poorly preserved or absent among Mississippian tetrapods. In particular, hindlimbs with a complete or near-complete array of tarsal elements and digits are notably rare. The unusual construction of the pes of Termonerpeton prompted us to examine the hindlimb morphology of six other East Kirkton tetrapods (Fig. 4a–g) alongside a selection of additional, mostly Carboniferous taxa (Fig. 4h–n). We focus on epipodials, tarsi, phalangeal formulae and digit length and proportions. To facilitate visual inspection of these elements, all hindlimbs are drawn to a common tibial length, except for the stem diapsid Petrolacosaurus, in which the epipodials are greatly elongate.Fig. 4: Comparison of the left tibia, fibula, tarsus, and digits of early tetrapods.a Balanerpeton after 2, b Eucritta after 12, c Eldeceeon after 6, d Silvanerpeton after 4, e Westlothiana after 7, f Kirktonecta original, see 15 (the grey area marks the estimated position and extent of the tarsus), g Termonerpeton, h Pederpes after 24, i, Greererpeton after 27, j Caerorhachis after 31, k Archeria after 30, l Hylonomus after 28, m Tuditanus after 22, n Petrolacosaurus after 29. Drawn to the same tibial length apart from n. Scale bars 10 mm.Full size imageIn terms of pes size relative to the tibia, the East Kirkton taxa Balanerpeton, Eucritta, and Silvanerpeton (Fig. 4a, b, d) are similarly proportioned. In contrast, Eldeceeon and Westlothiana (Fig. 4c, e) exhibit somewhat larger pedes. Kirktonecta has proportionally the largest pedes of all (Fig. 4f). Termonerpeton (Fig. 4g) has a pes of similar size to the first three taxa except that digit IV is relatively much longer than in any of the others, with an exceptionally large metatarsal IV. In all those taxa in which digit IV is fully preserved, it is the longest, especially in Eldeceeon and Kirktonecta, but in none does it approach in size and proportions that of Termonerpeton. The illustrated limbs also differ from one another in the degree of ossification of the tarsal bones. Most taxa except Eucritta have some indication of ossified tarsal elements, and some of them, including Balanerpeton and Silvanerpeton, show a complete or almost complete tarsal set. Kirktonecta does have an ossified tarsus, but specimen preservation does not allow us to identify individual elements. The phalangeal count, where known, also varies: 22343 in Balanerpeton2; 223?? in Eucritta12; 23455 in Silvanerpeton4; 23454 in Eldeceeon6, Kirktonecta15, Termonerpeton, and Westlothiana7.In addition, we compared the pedes of East Kirkton tetrapods with those of seven other taxa (Fig. 4h–n): one earlier, Pederpes24; one almost contemporary, Caerorhachis25; four later Carboniferous, Greererpeton26, Hylonomus27, Tuditanus22, and Petrolacosaurus28; and one early Permian, Archeria29. Of these, Greererpeton has relatively the smallest pes. In most, digit IV is the longest, though in Pederpes and Caerorhachis it is incomplete. The pes of Caerorhachis was originally restored with only three phalanges in digit IV30. This is probably incorrect and would be unusual in Carboniferous tetrapods. The pes of the anthracosaur Archeria was originally reconstructed with digit V as the longest29, but again this is unusual among later Carboniferous and early Permian tetrapods and we suspect that digits IV and V have been transposed, and Romer himself expressed doubt about this reconstruction29. In either case, the phalangeal formula of Archeria is similar to that of the East Kirkton anthracosaur Silvanerpeton, as 23455.Among Carboniferous tetrapods, temnospondyls such as Balanerpeton and colosteids such as Greererpeton show a digit IV that is somewhat longer than the others, but metatarsal IV is very similar in length and breadth to the adjacent metatarsals. In anthracosaurs, digit IV is the longest, but again metatarsal IV is not significantly broader than adjacent metatarsals. This is also the case in the early amniote Hylonomus and the microsaur Tuditanus. Among the taxa illustrated here, Termonerpeton shows a strikingly similar pes to that of the Late Pennsylvanian araeoscelidian diapsid Petrolacosaurus (Fig. 4n). In both, metatarsal IV is significantly longer and stouter than others and forms part of a similarly long digit IV. In early amniotes, an elongate digit IV coupled with an elongate metatarsal IV is a common occurrence in other taxa, such as protothyridids (e.g. Anthracodromeus31), basal araeoscelidians (e.g. Spinoaequalis32), younginids (e.g. Youngina33), saurians33, and basal synapsids (e.g. Heleosaurus34,35,36), among others.Based upon available evidence, an elongate digit IV is likely to be the plesiomorphic condition for crown amniotes, being present in Hylonomus, Paleothyris, and Petrolacosaurus (Fig. 4l, n), and shortening of this digit certainly represents a derived feature. In later crown amniotes, the conditions vary, with larger, heavier-bodied tetrapods such as dicynodonts and diadectids having generally shorter toes and adopting a more clearly plantigrade posture. An elongate metatarsal IV and associated digit, however, are not universal among Palaeozoic amniotes, and modifications of these conditions occur repeatedly across clades. For instance, in the eureptile captorhinid Eocaptorhinus, digit IV is also the longest, but the length of metatarsal IV does not greatly exceed that of other metatarsals37. The same is true of some early Permian clades, including seymouriamorphs (e.g. Seymouria38; Discosauriscus39), and diadectids (e.g. Diadectes40), although in the diadectomorph Orobates digit III is a little longer than digit IV41. Among synapsids, dicynodonts such as Diictodon42 and caseids43, to name a few, have five pedal digits of approximately uniform length.We further point out that, while digit IV attains a certain degree of elongation in other early tetrapod groups, such as temnospondyls, in none of them do the relative proportions of this digit (where known) compare to those of several stem and crown amniotes (Fig. 4).Phylogenetic relationshipsThe results of various phylogenetic analyses lend some support to the interpretation of Termonerpeton as a stem amniote, despite its uncertain placement in the unweighted character parsimony analysis (Fig. 5a). In the latter analysis, Termonerpeton appears in a polytomous node alongside baphetids (Eucritta; Baphetes; Megalocephalus), temnospondyls (Balanerpeton; Dendrysekos), the anthracosauroids Eldeceeon and Silvanerpeton, and the problematic Caerorhachis. In all other analyses—implied weights, reweighted characters, and Bayesian—Termonerpeton is placed on the amniote stem group, albeit in different positions, among a diverse array of ‘reptiliomorph’ clades and grades. In the implied weights analysis (Fig. 5b), Termonerpeton, Silvanerpeton, and Eldeceeon form a monophyletic group branching crownward of chroniosaurs plus anthracosaurs and anti-crownward of paraphyletic gephyrostegids. In the reweighted analysis (Fig. 5c), Termonerpeton and Caerorhachis appear as successive sister taxa, in that order, to monophyletic anthracosaurs. In the Bayesian analysis (Fig. 5d), the amniote total group receives moderate support with a credibility value (c.v.) of 76 with Caerorhachis as the most plesiomorphic stem amniote. Crownward of Caerorhachis is a polytomy with low support (c.v. = 59) that subtends Termonerpeton, a clade consisting of Eldeceeon plus Silvanerpeton, a clade of anthracosaurs, and a clade that includes all remaining taxa. In crownward succession, these taxa include chroniosaurs, gephyrostegids, seymouriamorphs, Solenodonsaurus, and Westlothiana as successive sister groups to a strongly supported (c.v. = 100) clade containing diadectomorphs, synapsids, and eureptiles. Although eureptile monophyly is not retrieved, strong support (c.v. = 100) is given to the branch subtending diadectomorphs plus synapsids44.Fig. 5: Results of phylogenetic analyses.a Strict consensus of 120 shortest trees from unweighted analysis (tree length = 1286 steps, ensemble consistency index C.I. = 0.2738 without uninformative characters, ensemble retention index R.I. = 0.5768), b Single tree from implied weights analysis (tree length = 1298 steps, Goloboff fit = −202.59266, C.I. = 0.2712, R.I. = 0.5713), c Single tree from reweighted analysis (tree length = 212,68965 steps, C.I. = 0.4755, R.I. = 0.774), d Bayesian topology with branches reporting credibility values.Full size image More

Lotsy, J. P. Evolution by Means of Hybridization (Martinus Nijhoff, 1916).Abbott, R. J. et al. Hybridization and speciation. J. Evol. Biol. 26, 229–246 (2013).CAS 
PubMed 
Article 

Google Scholar 
Schumer, M., Rosenthal, G. G. & Andolfatto, P. How common is homoploid hybrid speciation? Evolution 68, 1553–1560 (2014).PubMed 
Article 

Google Scholar 
Payseur, B. A. & Rieseberg, L. H. A genomic perspective on hybridization and speciation. Mol. Ecol. 25, 2337–2360 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Wang, Z. F. et al. Hybrid speciation via inheritance of alternate alleles of parental isolating genes. Mol. Plant 14, 208–222 (2021).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
Müntzing, A. Outlines to a genetic monograph for the genus Galeopsis: with special reference to the nature and inheritance of partial sterility. Hereditas 13, 185–341 (1930).Article 

Google Scholar 
Schumer, M., Cui, R., Rosenthal, G. G. & Andolfatto, P. Reproductive isolation of hybrid populations driven by genetic incompatibilities. Plos. Genet. 11, e1005041 (2015).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Taylor, S. A. & Larson, E. L. Insights from genomes into the evolutionary importance and prevalence of hybridization in nature. Nat. Ecol. Evol. 3, 170–177 (2019).PubMed 
Article 
PubMed Central 

Google Scholar 
Kong, S. & Kubatko, L. S. Comparative performance of popular methods for hybrid detection using genomic data. Syst. Biol. 70, 891–907 (2021).PubMed 
Article 
PubMed Central 

Google Scholar 
Goulet, B. E., Roda, F. & Hopkins, R. Hybridization in plants: old ideas, new techniques. Plant Physiol. 173, 65–78 (2016).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Jiang, Y. F. et al. Differentiating homoploid hybridization from ancestral subdivision in evaluating the origin of the D lineage in wheat. N. Phytol. 228, 409–414 (2020).Article 

Google Scholar 
Rokas, A. & Holland, P. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15, 454–459 (2000).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
Bapteste, E. & Philippe, H. The potential value of indels as phylogenetic markers: position of trichomonads as a case study. Mol. Biol. Evol. 19, 972–977 (2002).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
Mavárez, J. et al. Speciation by hybridization in Heliconius butterflies. Nature 441, 868–871 (2006).ADS 
PubMed 
Article 
CAS 
PubMed Central 

Google Scholar 
Lamichhaney, S. et al. Rapid hybrid speciation in Darwin’s finches. Science 359, 224–228 (2018).ADS 
CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
Zhang, B. W. et al. Phylogenomics reveals an ancient hybrid origin of the Persian walnut. Mol. Biol. Evol. 36, 2451–2461 (2019).CAS 
Article 

Google Scholar 
Guo, X., Thomas, D. C. & Saunders, R. M. K. Gene tree discordance and coalescent methods support ancient intergeneric hybridisation between Dasymaschalon and Friesodielsia (Annonaceae). Mol. Phylogenet. Evol. 127, 14–29 (2018).PubMed 
Article 
PubMed Central 

Google Scholar 
Winkler, H. Betulaceae. In: Pflanzenreich IV (Verlag von Wilhelm Engelmann, 1904).Li, P. Q. & Skvortsov, A. K. Betulaceae. In: Flora of China (Science Press & Missouri Botanical Garden Press, 1999).Crane, P. R. Betulaceous leaves and fruits from the British Upper Palaeocene. Bot. J. Linn. Soc. 83, 103–136 (1981).Article 

Google Scholar 
Li, P. Q. & Cheng, S. X. Betulaceae. In: Flora Reipublicae Popularis Sinicae (Science Press, 1979).Yoo, K. O. & Wen, J. Phylogeny and biogeography of Carpinus and subfamily Coryloideae (Betulaceae). Int. J. Plant Sci. 163, 641–650 (2002).Article 

Google Scholar 
Li, J. H. Sequences of low-copy nuclear gene support the monophyly of Ostrya and paraphyly of Carpinus (Betulaceae). J. Sys. Evol. 46, 333–340 (2008).
Google Scholar 
Yang, X. Y. et al. Plastomes of Betulaceae and phylogenetic implications. J. Sys. Evol. 57, 508–518 (2019).Article 

Google Scholar 
Yang, Y. Z. et al. Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana. Nat. Commun. 9, 5449 (2018).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Yang, X. Y. et al. A chromosome-level reference genome of the hornbeam, Carpinus fangiana. Sci. Data 7, 24 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Li, Y. et al. The Corylus mandshurica genome provides insights into the evolution of Betulaceae genomes and hazelnut breeding. Hortic. Res. 8, 54 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Salojärvi, J. et al. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nat. Genet. 49, 904–912 (2017).PubMed 
Article 
CAS 

Google Scholar 
Tajima, F. Evolutionary relationship of DNA-sequences in finite populations. Genetics 105, 437–460 (1983).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Durand, E. Y., Patterson, N., Reich, D. & Slatkin, M. Testing for ancient admixture between closely related populations. Mol. Biol. Evol. 28, 2239–2252 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Blischak, P. D., Chifman, J., Wolfe, A. D. & Kubatko, L. S. HyDe: a Python package for genome-scale hybridization detection. Syst. Biol. 67, 821–829 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Kubatko, L. S. & Chifman, J. An invariants-based method for efficient identification of hybrid species from large-scale genomic data. BMC Evol. Biol. 19, 112 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Baack, E., Melo, M. C., Rieseberg, L. H. & Ortiz-Barrientos, D. The origins of reproductive isolation in plants. N. Phytol. 207, 968–984 (2015).Article 

Google Scholar 
Sobel, J. M. & Chen, G. F. Unification of methods for estimating the strength of reproductive isolation. Evolution 68, 1511–1522 (2014).PubMed 
Article 

Google Scholar 
Imura, Y. et al. CRYPTIC PRECOCIOUS/MED12 is a novel flowering regulator with multiple target steps in Arabidopsis. Plant Cell Physiol. 53, 287–303 (2012).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Kim, S.-J. & Bassham, D. C. TNO1 is involved in salt tolerance and vacuolar trafficking in Arabidopsis. Plant Physiol. 156, 514–526 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zhang, F. et al. Control of leaf blade outgrowth and floral organ development by LEUNIG, ANGUSTIFOLIA3 and WOX transcriptional regulators. N. Phytol. 223, 2024–2038 (2019).CAS 
Article 

Google Scholar 
Liu, Z. C., Franks, R. G. & Klink, V. P. Regulation of gynoecium marginal tissue formation by LEUNIG and AINTEGUMENTA. Plant Cell 12, 1879–1891 (2000).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sitaraman, J., Bui, M. & Liu, Z. LEUNIG_HOMOLOG and LEUNIG perform partially redundant functions during Arabidopsis embryo and floral development. Plant Physiol. 147, 672–681 (2008).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Chen, C. L. et al. Phylotranscriptomics reveals extensive gene duplication in the subtribe Gentianinae (Gentianaceae). J. Sys. Evol. 59, 1198–1208 (2021).Article 

Google Scholar 
Morales-Briones, D. F. et al. Disentangling sources of gene tree discordance in phylogenomic data sets: testing ancient hybridizations in Amaranthaceae s.l. Syst. Biol. 70, 219–235 (2021).PubMed 
Article 
PubMed Central 

Google Scholar 
Yang, Y. Z. et al. Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution. Nat. Plants 6, 215–222 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Stull, G. W. et al. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms. Nat. Plants 7, 1015–1025 (2021).PubMed 
Article 
PubMed Central 

Google Scholar 
Luo, X. et al. Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor. Mol. Ecol. 26, 3037–3049 (2017).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
Grover, C. E. et al. Re-evaluating the phylogeny of allopolyploid Gossypium L. Mol. Phylogenet. Evol. 92, 45–52 (2015).PubMed 
Article 
PubMed Central 

Google Scholar 
Edger, P. P., McKain, M. R., Bird, K. A. & VanBuren, R. Subgenome assignment in allopolyploids: challenges and future directions. Curr. Opin. Plant Biol. 42, 76–80 (2018).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
Doyle, J. J. & Doyle, J. L. A rapid DNA isolation procedure for small amounts of fresh leaf tissue. Phytochem. Bull. 19, 11–15 (1987).
Google Scholar 
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. Plos ONE 9, e112963 (2014).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119–1125 (2013).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinf. 5, 4.10.1–4.10.14 (2004).Article 

Google Scholar 
Haas, B. J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435–W439 (2006).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Birney, E., Clamp, M. & Durbin, R. GeneWise and genomewise. Genome Res. 14, 988–995 (2004).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7 (2008).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45–48 (2000).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Marchler-Bauer, A. et al. CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res. 39, D225–D229 (2011).CAS 
PubMed 
Article 
PubMed Central 

Google Scholar 
Hunter, S. et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 37, D211–D215 (2009).CAS 
Article 

Google Scholar 
Conesa, A. & Götz, S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics 2008, 619832 (2008).PubMed 
Article 
CAS 
PubMed Central 

Google Scholar 
Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C. & Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182–W185 (2007).PubMed 
PubMed Central 
Article 

Google Scholar 
Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ye, G. et al. De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia provides insight into secondary growth. Plant J. 97, 779–794 (2019).CAS 
PubMed 
Article 

Google Scholar 
Marrano, A. et al. High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome. GigaScience 9, giaa050 (2020).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Löytynoja, A. Phylogeny-aware alignment with PRANK. In: Multiple Sequence Alignment Methods, Methods in Molecular Biology (Humana Press, 2014).Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Wang, Y. P. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Kielbasa, S. M., Wan, R., Sato, K., Horton, P. & Frith, M. C. Adaptive seeds tame genomic sequence comparison. Genome Res. 21, 487–493 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform. 19, 153 (2018).Article 

Google Scholar 
Sukumaran, J. & Holder, M. T. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26, 1569–1571 (2010).CAS 
PubMed 
Article 

Google Scholar 
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Malinsky, M., Matschiner, M. & Svardal, H. Dsuite—Fast D-statistics and related admixture evidence from VCF files. Mol. Ecol. Resour. 21, 584–595 (2021).PubMed 
Article 

Google Scholar 
Hudson, R. R., Kreitman, M. & Aguadé, M. A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153–159 (1987).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar  More

Mao, Y. et al. Bivalve production in China (eds. Smaal, A., Ferreira, J., Grant, J., Petersen, J, & Strand, Ø.) 51–72 (Springer, New York, 2019).CFSY. China fishery statistical yearbook. (China Agriculture Publishing House, Beijing, 2021).Muller-Feuga, A. Microalgae for aquaculture: the current global situation and future trends (ed. Richmond, A.) 352–364 (Blackwell Science, Hoboken, 2004).Lindahl, O. Mussel farming as a tool for re‐eutrophication of coastal waters: experiences from Sweden (ed. Shumway, S. E.) 217–237 (Wiley-Blackwell, Hoboken, 2011).Petersen, J. K., Hasler, B., Timmermann, K., Nielsen, P. & Holmer, M. Mussels as a tool for mitigation of nutrients in the marine environment. Mar. Pollut. Bull. 82, 137–143 (2014).CAS 

Google Scholar 
Petersen, J. K., Saurel, C., Nielsen, P. & Timmermann, K. The use of shellfish for eutrophication control. Aquacult. Int. 24, 857–878 (2016).
Google Scholar 
Hily, C., Grall, J., Chauvaud, L., Lejart, M. & Clavier, J. CO2 generation by calcified invertebrates along rocky shores of Brittany, France. Mar. Freshwater. Res. 64, 91–101 (2013).CAS 

Google Scholar 
Filgueira, R. Strohmeier, T. & Strand, Ø. Regulating services of bivalve molluscs in the context of the carbon cycle and implications for ecosystem valuation (eds. Smaal, A., Ferreira, J., Grant, J., Petersen, J. & Strand, Ø.) 231–251 (Springer, New York, 2019).Newell, R. I. Ecosystem influences of natural and cultivated populations of suspension-feeding bivalve molluscs: a review. J. Shellfish. Res. 23, 51–62 (2004).
Google Scholar 
Benemann, J. R. Microalgae aquaculture feeds. J. Appl. Phycol. 4, 233–245 (1992).
Google Scholar 
Brown, M. R. & Blackburn, I. Live microalgae as feeds in aquaculture hatcheries (eds. Allan, G. & Burnell, G.) 117–156 (Woodhead Publishing Series in Food Science, Technology and Nutrition, 2013).Thajuddin, N. & Subramanian, G. Cyanobacterial biodiversity and potential applications in biotechnology. Curr. Sci. 89, 47–57 (2005).CAS 

Google Scholar 
Caers, M., Coutteau, P. & Sorgeloos, P. Dietary impact of algal and artificial diets, fed at different feeding rations, on the growth and fatty acid composition of Tapes philippinarum (L.) spat. Aquaculture 170, 307–322 (1999).CAS 

Google Scholar 
Chen, S. M., Tseng, K. Y. & Huang, C. H. Fatty acid composition, sarcoplasmic reticular lipid oxidation, and immunity of hard clam (Meretrix lusoria) fed different dietary microalgae. Fish. Shellfish. Immunol. 45, 141–145 (2015).CAS 

Google Scholar 
Rosa, M., Ward, J. E. & Shumway, S. E. Selective capture and ingestion of particles by suspension-feeding bivalve molluscs: a review. J. Shellfish. Res. 37, 727–746 (2018).
Google Scholar 
Ward, J. E. & Shumway, S. E. Separating the grain from the chaff: particle selection in suspension-and deposit-feeding bivalves. J. Exp. Mar. Biol. Ecol. 300, 83–130 (2004).
Google Scholar 
Tang, B., Liu, B., Wang, G., Tao, Z. & Xiang, J. Effects of various algal diets and starvation on larval growth and survival of Meretrix meretrix. Aquaculture 254, 526–533 (2006).
Google Scholar 
Espinosa, E. P., Cerrato, R. M., Wikfors, G. H. & Allam, B. Modeling food choice in the two suspension-feeding bivalves, Crassostrea virginica and Mytilus edulis. Mar. Biol. 163, 1–13 (2016).
Google Scholar 
Jones, J., Allam, B. & Espinosa, E. P. Particle selection in suspension-feeding bivalves: does one model fit all?. Biol. Bull. 238, 41–53 (2020).CAS 

Google Scholar 
Pales Espinosa, E., Cerrato, R. M., Wikfors, G. H. & Allam, B. Modeling food choice in the two suspension-feeding bivalves, Crassostrea virginica and Mytilus edulis. Mar. Biol. 163, 1–13 (2016).CAS 

Google Scholar 
Barillé, L., Prou, J., Héral, M. & Bourgrier, S. No influence of food quality, but ration-dependent retention efficiencies in the Japanese oyster Crassostrea gigas. J. Exp. Mar. Biol. Ecol. 171, 91–106 (1993).
Google Scholar 
Petersen, J. K. et al. Intercalibration of mussel Mytilus edulis clearance rate measurements. Mar. Ecol. Prog. Ser. 267, 187–194 (2004).ADS 

Google Scholar 
Zhang, T. et al. Effects of environmental factors on the survival and growth of juvenile hard clam Mercenaria mercenaria (Linnaeus,1758). Oceanol. Limnol. Sin. 34, 142–149 (2003).
Google Scholar 
Matias, D. et al. The influence of different microalgal diets on European clam (Ruditapes decussatus, Linnaeus, 1758) larvae culture performances. Aquacult. Res. 46, 2527–2543 (2015).
Google Scholar 
Liao, K. et al. qPCR analysis of bivalve larvae feeding preferences when grazing on mixed microalgal diets. PLoS ONE 12, e0180730 (2017).
Google Scholar 
Sautour, B., Artigas, L. F., Delmas, D., Herbland, A. & Laborde, P. Grazing impact of micro- and mesozooplankton during a spring situation in coastal waters off the Gironde estuary. J. Plankton. Res. 22, 531–552 (2000).
Google Scholar 
Manoylov, K. M. Taxonomic identification of algae (morphological and molecular): species concepts, methodologies, and their implications for ecological bioassessment. J. Phycol. 50, 409–424 (2014).
Google Scholar 
Shokralla, S. et al. Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Mol. Ecol. Resour. 14, 892–901 (2014).CAS 

Google Scholar 
Hirai, J., Hidaka, K., Nagai, S. & Ichikawa, T. Molecular-based diet analysis of the early post-larvae of Japanese sardine Sardinops melanostictus and Pacific round herring Etrumeus teres. Mar. Ecol. Prog. Ser. 564, 99–113 (2017).ADS 
CAS 

Google Scholar 
Su, M., Liu, H., Liang, X., Gui, L. & Zhang, J. Dietary analysis of marine fish species: enhancing the detection of prey-specific dna sequences via high-throughput sequencing using blocking primers. Estuar. Coast. 41, 560–571 (2018).
Google Scholar 
Talwar, C., Nagar, S., Lal, R. & Negi, R. K. Fish gut microbiome: current approaches and future perspectives. Indian J. Microbiol. 58, 397–414 (2018).CAS 

Google Scholar 
Yi, X. et al. In situ diet of the copepod Calanus sinicus in coastal waters of the South Yellow Sea and the Bohai Sea. Acta. Oceanol. Sin. 36, 68–79 (2017).CAS 

Google Scholar 
Reis, A. D., Jeffs, A. G. & Lavery, S. D. From feeding habits to food webs: exploring the diet of an opportunistic benthic generalist. Mar. Ecol. Prog. Ser. 655, 107–121 (2020).ADS 

Google Scholar 
Yeh, H. D., Questel, J. M., Maas, K. R. & Bucklin, A. Metabarcoding analysis of regional variation in gut contents of the copepod Calanus finmarchicus in the North Atlantic Ocean. Deep Sea Res. II 180, 104738 (2020).
Google Scholar 
Zeale, M. R., Howeverlin, R. K., Barker, G. L., Lees, D. C. & Jones, G. Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces. Mol. Ecol. Resour. 11, 236–244 (2011).CAS 

Google Scholar 
Sherwood, A. R. & Presting, G. G. Universal primers amplify a 23s rDNA plastid marker in eukaryotic algae and cyanobacteria. J. Phycol. 43, 605–608 (2007).
Google Scholar 
Qiao, L., Chang, Z., Li, J. & Chen, Z. Phytoplankton community succession in relation to water quality changes in the indoor industrial aquaculture system for Litopenaeus vannamei. Aquaculture 527, 735441 (2020).CAS 

Google Scholar 
Vahl, O. Efficiency of particle retention in Mytilus edulis L. Ophelia 10, 17–25 (1972).
Google Scholar 
Riisgård, H. U. Efficiency of particle retention and filtration rate in 6 species of northeast American bivalves. Mar. Ecol. Prog. Ser. 45, 217–223 (1988).ADS 

Google Scholar 
Rosa, M. et al. Examining the physiological plasticity of particle capture by the blue mussel, Mytilus edulis (L.): confounding factors and potential artifacts with studies utilizing natural seston. J. Exp. Mar. Biol. Ecol. 473, 207–217 (2015).
Google Scholar 
Shumway, S. E. et al. Flow cytometry: a new method for characterization of differential ingestion, digestion and egestion by suspension feeders. Mar. Ecol. Prog. Ser. 24, 201–204 (1985).ADS 

Google Scholar 
Dupuy, C. et al. Feeding rate of the oyster Crassostrea gigas in a natural planktonic community of the mediterranean thau lagoon. Mar. Ecol. Prog. Ser. 205, 171–184 (2000).ADS 

Google Scholar 
Strøhmeier, T., Strand, Ø., Alunno-Bruscia, M., Duinker, A. & Cranford, P. J. Variability in particle retention efficiency by the mussel Mytilus edulis. J. Exp. Mar. Biol. Ecol. 412, 96–102 (2012).
Google Scholar 
Yahel, G., Marie, D., Beninger, P. G., Eckstein, S. & Genin, A. In situ evidence for pre-capture qualitative selection in the tropical bivalve Lithophaga simplex. Aquat. Biol. 6, 235–246 (2009).
Google Scholar 
Bass, A. E., Malouf, R. E. & Shumway, S. E. Growth of northern quahogs, Mercenaria mercenaria (Linnaeus, 1758) fed on picophytoplankton. J. Shellfish. Res. 9, 299–307 (1990).
Google Scholar 
Leblanc, A. et al. Determination of isotopic labeling of proteins by precursor ion scanning liquid chromatography/tandem mass spectrometry of derivatized amino acids applied to nuclear magnetic resonance studies. Rapid Commun. Mass. Spectrom. 26, 1165–1174 (2012).ADS 
CAS 

Google Scholar 
Sonier, R. et al. Picoplankton contribution to Mytilus edulis growth in an intense culture environment. Mar. Biol. 163, 73–85 (2016).
Google Scholar 
Herdman, M., Castenholz, R. W., Waterbury, J. B. & Rippka, R. Form-genus XIII. Synechococcus (eds. Boone, D. R. & Castenholz, R. W.) 508–512 (Springer, New York, 2001).Hibberd, D. J. Notes on the taxonomy and nomenclature of the algal classes Eustigmatophyceae and Tribophyceae (synonym Xanthophyceae). Bot. J. Linn. Soc. 82, 93–119 (1981).
Google Scholar 
Wei, Y. Chrysochromulina parva Lackey Prymnesiophyceae new record in China and its seasonal fluctuation in Lake Donghu, Wuhan. Acta Hydrobiol. Sin. 20, 317–321 (1996).
Google Scholar 
Stockner, J. G. & Antia, N. J. Algal picoplankton from marine and freshwater ecosystems: a multidisciplinary perspective. Can. J. Fish. Aquat. Sci. 43, 2472–2503 (1986).
Google Scholar 
Gallager, S., Waterbury, J. & Stoecker, D. Efficient grazing and utilization of the marine cyanobacterium Synechococcus sp. by larvae of the bivalve Mercenaria mercenaria. Mar. Biol. 119, 251–259 (1994).
Google Scholar 
Seychelles, L. H., Audet, C., Tremblay, R., Fournier, R. & Pernet, F. Essential fatty acid enrichment of cultured rotifers (Brachionus plicatilis, Müller) using frozen-concentrated microalgae. Aqua. Nut. 15, 431–439 (2009).CAS 

Google Scholar 
Hughes, T. G. The sorting of food particles by Abra sp. (bivalvia: tellinacea). J. Exp. Mar. Biol. Ecol. 20, 137–156 (1975).
Google Scholar 
Hernroth, B., Larsson, A. & Edebo, L. Influence on uptake, distribution and elimination of Salmonella typhimurium in the blue mussel, Mytilus edulis, by the cell surface properties of the bacteria. J. Shellfish. Res. 19, 167–174 (2000).
Google Scholar 
Rosa, M. et al. Effects of particle surface properties on feeding selectivity in the eastern oyster Crassostrea virginica and the blue mussel Mytilus edulis. J. Exp. Mar. Biol. Ecol. 446, 320–327 (2013).
Google Scholar 
Rosa, M., Ward, J. E., Holohan, B. A., Shumway, S. E. & Wikfors, G. H. Physicochemical surface properties of microalgae and their combined effects on particle selection by suspension-feeding bivalve molluscs. J. Exp. Mar. Biol. Ecol. 486, 59–68 (2017).CAS 

Google Scholar 
Grasland, B., Mitalane, J., Briandet, R., Quemener, E. & Haras, D. Bacterial biofilm in seawater: cell surface properties of early-attached marine bacteria. Biofouling 19, 307–313 (2003).CAS 

Google Scholar 
Ozkan, A. & Berberoglu, H. Physico-chemical surface properties of microalgae. Colloids. Surf. B. 112, 287–293 (2013).CAS 

Google Scholar 
Dadon-Pilosof, A. et al. Surface properties of SAR 11 bacteria facilitate grazing avoidance. Nat. Microbiol. 2, 1608–1615 (2017).
Google Scholar 
Xiao, G., Zhang, J., Cai, X., Lu, R. & Fang, J. Studies on the filtration feeding, respiration ration and excretion of Ruditapes philippinarum juvenile. J. Oceanogr. Taiwan Strait 25, 30–35 (2006).
Google Scholar 
Atkins, D. On the ciliary mechanisms and interrelationships of lamellibranchs. VII: latero-frontal cilia of the gill filaments and their phylogenetic value. Q. J. Microsc. Sci. 80, 345–433 (1938).
Google Scholar 
Owen, G. & Mccrae, J. M. Further studies on the latero-frontal tracts of bivalves. Proc. R. Soc. London. 194, 527–544 (1976).ADS 

Google Scholar 
Owen, G. Classification and the bivalve gill. Phil. Trans. R. Soc. Lond. 284, 377–385 (1978).
Google Scholar 
Ward, J. E., Sanford, L. P. & Newell, R. A new explanation of particle capture in suspension- feeding bivalve molluscs. Limnol. Oceanogr. 43, 741–752 (1998).ADS 

Google Scholar 
Winter, J. E. A review on the knowledge of suspension-feeding in lamellibranchiate bivalves, with special reference to artificial aquaculture systems. Aquaculture 13, 1–33 (1978).
Google Scholar 
Newell, C. R., Wildish, D. J. & Macdonald, B. A. The effects of velocity and seston concentration on the exhalant siphon area, valve gape and filtration rate of the mussel Mytilus edulis. J. Exp. Mar. Biol. Ecol. 262, 91–111 (2001).
Google Scholar 
Jacobs, P., Troost, K., Riegman, R., Van der, M. & J.,. Length- and weight-dependent clearance rates of juvenile mussels (Mytilus edulis) on various planktonic prey items. Helgol. Mar. Res. 69, 101–112 (2015).ADS 

Google Scholar 
Ivlev, V. S. Experimental ecology of the feeding of fish. (Yale University Press New Haven, Connecticut, 1961) p 302.Strauss, R. E. Reliability estimates for Ivlevs electivity index the forage ratio and a proposed linear index of food selection. Trans. Am. Fish. Soc. 108, 344–352 (1979).
Google Scholar 
Puig, S., Videla, F., Cona, M. I. & Monge, A. S. Use of food availability by guanacos (Lama guanicoe) and livestock in Northern Patagonia (Mendoza, Argentina). J. Arid. Environ. 47, 291–308 (2001).ADS 

Google Scholar  More

Beyaert, I. & Hilker, M. Plant odour plumes as mediators of plant–insect interactions. Biol. Rev. 89, 68–81 (2014).
Google Scholar 
Simpraga, M., Takabayashi, J. & Holopainen, J. K. Language of plants: Where is the word?. J. Integr. Plant Biol. 58, 343–349 (2016).CAS 

Google Scholar 
Bruce, T. J. A., Wadhams, L. J. & Woodcock, C. M. Insect host location: A volatile situation. Trends Plant Sci. 10, 269–274 (2005).CAS 

Google Scholar 
Bruce, T. J. A. & Pickett, J. A. Perception of plant volatile blends by herbivorous insects—Finding the right mix. Phytochemistry 72, 1605–1611 (2011).CAS 

Google Scholar 
Raguso, R. A. Wake up and smell the roses: The ecology and evolution of floral scent. Annu. Rev. Ecol. Evol. S. 39, 549–569 (2008).
Google Scholar 
Schiestl, F. P. The evolution of floral scent and insect chemical communication. Ecol. Lett. 13, 643–656 (2010).
Google Scholar 
Arimura, G., Kost, C. & Boland, W. Herbivore-induced, indirect plant defences. Biochim. Biophys. Acta. 1734, 91–111 (2005).CAS 

Google Scholar 
Hare, J. D. Ecological role of volatiles produced by plants in response to damage by herbivorous insects. Annu. Rev. Entomol. 56, 161–180 (2011).CAS 

Google Scholar 
Laothawornkitkul, J., Taylor, J. E., Paul, N. D. & Hewitt, C. N. Biogenic volatile organic compounds in the earth system. New Phytol. 183, 27–51 (2009).CAS 

Google Scholar 
Dicke, M., van Loon, J. J. A. & Soler, R. Chemical complexity of volatiles from plant induced by multiple attack. Nature Chem. Biol. 5, 317–324 (2009).CAS 

Google Scholar 
Loreto, F. & Schnitzler, J. P. Abiotic stresses and induced BVOCs. Trends Plant Sci. 15, 154–166 (2010).CAS 

Google Scholar 
Tasin, M. et al. Synergism and redundancy in a plant volatile blend attracting grapevine moth females. Phytochemistry 68, 203–209 (2007).CAS 

Google Scholar 
Riffell, J. A., Lei, H., Christensen, T. A. & Hildebrand, J. G. Characterization and coding of behaviorally significant odor mixtures. Curr. Biol. 19, 335–340 (2009).CAS 

Google Scholar 
Riffell, J. A., Lei, H. & Hildebrand, J. G. Neural correlates of behavior in the moth Manduca sexta in response to complex odors. Proc. Natl. Acad. Sci. USA 106, 19219–19226 (2009).ADS 
CAS 

Google Scholar 
Atema, J. Eddy chemotaxis and odor landscapes: Exploration of nature with animal sensors. Biol. Bull. 191, 129–138 (1996).CAS 

Google Scholar 
Conchou, L. et al. Insect odorscapes: From plant volatiles to natural olfactory scenes. Front. Physiol. 10, 972 (2019).
Google Scholar 
Riffell, J. A., Abrell, L. & Hildebrand, J. G. Physical processes and real-time chemical measurement of the insect olfactory environment. J. Chem. Ecol. 34, 837–853 (2008).CAS 

Google Scholar 
Mylne, K. R., Davidson, M. J. & Thomson, D. J. Concentration fluctuation measurements in tracer plumes using high and low frequency response detectors. Bound-Lay. Meteorol. 79, 225–242 (1996).ADS 

Google Scholar 
Finelli, C. M., Pentcheff, N. D., Zimmer-Faust, R. K. & Wethey, D. S. Odor transport in turbulent flows: Constraints on animal navigation. Limnol. Oceanogr. 44, 1056–1071 (1999).ADS 
CAS 

Google Scholar 
Murlis, J., Elkinton, J. S. & Cardé, R. T. Odor plumes and how insects use them. Annu. Rev. Entomol. 37, 505–532 (1992).
Google Scholar 
Murlis, J., Willis, M. A. & Cardé, R. T. Spatial and temporal structures of pheromone plumes in fields and forests. Physiol. Entomol. 25, 211–222 (2000).CAS 

Google Scholar 
Kennedy, J. S. The visual response of flying mosquitoes. Proc. Zool. Soc. London Ser. A 109, 221–242 (1940).
Google Scholar 
Bursell, E. Observations on the orientation of tsetse flies (Glossina pallidipes) to wind-borne odours. Physio. Entomol. 9, 133–137 (1984).
Google Scholar 
Murlis, J., Elkinton, J. S. & Cardé, R. T. Odor plumes and how insects use them. Annu. Rev. Entomol. 37, 505–532 (1992).
Google Scholar 
Kennedy, J. S., Ludlow, A. R. & Sanders, C. J. Guidance of flying male moths by wind-borne sex-pheromone. Physiol. Entomol. 6, 395–412 (1981).
Google Scholar 
Koehl, M. A. R. The fluid mechanics of arthropod sniffing in turbulent odor plumes. Chem. Senses 31, 93–105 (2006).CAS 

Google Scholar 
Baker, T. C., Willis, M. A., Haynes, K. F. & Phelan, P. L. A pulsed cloud of sex pheromone elicits upwind flight in male moths. Physiol. Entomol. 10, 257–265 (1985).
Google Scholar 
Willis, M. A. & Baker, T. C. Effects of intermittent and continuous pheromone stimulation on the flight behavior of the oriental fruit moth, Grapholita molesta. Physiol. Entomol. 9, 341–358 (1984).
Google Scholar 
Mafraneto, A. & Cardé, R. T. Fine-scale structure of pheromone plumes modulates upwind orientation of flying moths. Nature 369, 142–144 (1994).ADS 
CAS 

Google Scholar 
Mafraneto, A. & Cardé, R. T. Dissection of the pheromone-modulated flight of moths using single-pulse response as a template. Experientia 52, 373–379 (1996).CAS 

Google Scholar 
Vickers, N. J. & Baker, T. C. Reiterative responses to single strands of odor promote sustained upwind flight and odor source location by moths. Proc. Natl. Acad. Sci. USA 91, 5756–5760 (1994).ADS 
CAS 

Google Scholar 
Lei, H., Riffell, J. A., Gage, S. L. & Hildebrand, J. G. Contrast enhancement of stimulus intermittency in a primary olfactory network and its behavioral significance. J. Biol. 8, 21 (2009).
Google Scholar 
Kuenen, L. & Carde, R. T. Strategies for recontacting a lost pheromone plume: Casting and upwind flight in the male gypsy moth. Physiol. Entomol. 19, 15–29 (1994).
Google Scholar 
Vickers, N. J. & Baker, T. C. Latencies of behavioral response to interception of filaments of sex pheromone and clean air influence flight track shape in Heliothis virescens (F.) males. J. Comp. Physiol. A. 178, 831–847 (1996).
Google Scholar 
Vickers, N. J. Mechanisms of animal navigation in odor plumes. Biol. Bull. 198, 203–212 (2000).CAS 

Google Scholar 
Cardé, R. T. & Willis, M. A. Navigational strategies used by insects to find distant, wind-borne sources of odor. J. Chem. Ecol. 34, 854–866 (2008).
Google Scholar 
Willis, M. A. & Baker, T. C. Effects of varying sex pheromone component ratios on the zigzagging flight movements of the oriental fruit moth, Grapholita molesta. J. Insect. Behav. 1, 357–371 (1988).
Google Scholar 
Voskamp, K. E., Den Otter, C. J. & Noorman, N. Electroantennogram responses of tsetse flies (Glossina pallidipes) to host odours in an open field and riverine woodland. Physiol. Entomol. 23, 176–183 (1998).
Google Scholar 
Cai, X. M., Xu, X. X., Bian, L., Luo, Z. X. & Chen, Z. M. Measurement of volatile plant compounds in field ambient air by thermal desorption–gas chromatography–mass spectrometry. Anal. Bioanal. Chem. 407, 9105–9114 (2015).CAS 

Google Scholar 
Zollner, G. E., Torr, S. J., Ammann, C. & Meixner, F. X. Dispersion of carbon dioxide plumes in African woodland: implications for host-finding by tsetse flies. Physiol. Entomol. 29, 381–394 (2004).
Google Scholar 
McFrederick, Q. S., Kathilankal, J. C. & Fuentes, J. D. Air pollution modifies floral scent trails. Atmos. Environ. 42, 2336–2348 (2008).ADS 
CAS 

Google Scholar 
Yuan, J. S., Himanen, S. J., Holopainen, J. K., Chen, F. & NealStewart, C. Jr. Smelling global climate change: mitigation of function for plant volatile organic compounds. Trends Ecol. Evol. 24, 323–331 (2009).
Google Scholar 
Weissburg, M. J. The fluid dynamical context of chemosensory behavior. Biol. Bull. 198, 188–202 (2000).CAS 

Google Scholar 
Atkinson, R. & Arey, J. Gas-phase tropospheric chemistry of biogenic volatile organic compounds: A review. Atmos. Environ. 37, 197–219 (2003).ADS 

Google Scholar 
Helmig, D., Bocquet, F., Pollmann, J. & Revermann, T. Analytical techniques for sesquiterpene emission rate studies in vegetation enclosure experiments. Atmos. Environ. 38, 557–572 (2004).ADS 
CAS 

Google Scholar 
Riffell, J. A, Shlizerman, E., Sanders, E., Abrell, L., Medina, B., Hinterwirth, A. J. & NathanKutz, J. Flower discrimination by pollinators in a dynamic chemical environment. Science 344, 1515–1518 (2014).Shorey, H. H. Animal communication by pheromones (Academic Press, 1976).Cardé, R. T. & Charlton, R. E. Olfactory sexual communication in Lepidoptera: Strategy, sensitivity and selectivity In Insect communication (ed. Lewis, T.) 241–265 (Academic Press, 1984).Elkinton, J. S., Schal, C., Ono, T. & Carde, R. T. Pheromone puff trajectory and upwind flight of male gypsy moths in a forest. Physiol. Entomol. 12, 399–406 (1987).
Google Scholar 
Baker, T. C., Fadamiro, H. Y. & Cosse, A. A. Moth uses fine tuning for odour resolution. Nature 393, 530 (1998).ADS 
CAS 

Google Scholar 
Szyszka, P., Stierle, J. S., Biergans, S. & Galizia, C. G. The speed of smell: Odor-object segregation within milliseconds. PLoS One 7, e36096 (2012).ADS 
CAS 

Google Scholar 
Hildebrand, J. G. Analysis of chemical signals by nervous systems. Proc. Natl. Acad. Sci. USA 92, 67–74 (1995).ADS 
CAS 

Google Scholar 
Cai, X. M. et al. Field background odour should be taken into account when formulating a pest attractant based on plant volatiles. Sci. Rep. 7, 41818 (2017).ADS 
CAS 

Google Scholar 
Xu, X. X. et al. Does background odor in tea gardens mask attractants? Screening and application of attractants for Empoasca onukii Matsuda. J. Econ. Entomol. 110, 2357–2363 (2017).CAS 

Google Scholar 
Hare, J. D. & Sun, J. J. Production of induced volatiles by Datura wrightii in response to damage by insects: Effect of herbivore species and time. J. Chem. Ecol. 37, 751–764 (2011).CAS 

Google Scholar 
Mumm, R., Tiemann, T., Schulz, S. & Hilker, M. Analysis of volatiles from black pine (Pinus nigra): Significance of wounding and egg deposition by a herbivorous sawfly. Phytochemistry 65, 3221–3230 (2004).CAS 

Google Scholar  More

Franco FP, Túler AC, Gallan DZ, Gonçalves FG, Favaris AP, Peñaflor MFGV, et al. Fungal phytopathogen modulates plant and insect responses to promote its dissemination. ISME J. 2021;15:3522–33.CAS 

Google Scholar 
Huang H, Ren L, Li H, Schmidt A, Gershenzon J, Lu Y, et al. The nesting preference of an invasive ant is associated with the cues produced by actinobacteria in soil. PLoS Pathog. 2020;16:e1008800.CAS 

Google Scholar 
Angleró-Rodríguez YI, Blumberg BJ, Dong Y, Sandiford SL, Pike A, Clayton AM, et al. A natural Anopheles-associated Penicillium chrysogenum enhances mosquito susceptibility to Plasmodium infection. Sci Rep. 2016;6:34084.
Google Scholar 
Davis TS, Landolt PJ. A survey of insect assemblages responding to volatiles from a ubiquitous fungus in an agricultural landscape. J Chem Ecol. 2013;39:860–8.CAS 

Google Scholar 
Flury P, Vesga P, Dominguez-Ferreras A, Tinguely C, Ullrich CI, Kleespies RG, et al. Persistence of root-colonizing Pseudomonas protegens in herbivorous insects throughout different developmental stages and dispersal to new host plants. ISME J. 2018;13:860–72.
Google Scholar 
Kandasamy D, Gershenzon J, Andersson MN, Hammerbacher A. Volatile organic compounds influence the interaction of the Eurasian spruce bark beetle (Ips typographus) with its fungal symbionts. ISME J. 2019;13:1788–800.CAS 

Google Scholar 
Keesey IW, Koerte S, Khallaf MA, Retzke T, Guillou A, Grosse-Wilde E, et al. Pathogenic bacteria enhance dispersal through alteration of Drosophila social communication. Nat Commun. 2017;8:265.
Google Scholar 
Paul GB, Gerhard F, Elżbieta R, Alexandra S, Arne H, Sébastien L, et al. Yeast, not fruit volatiles mediate Drosophila melanogaster attraction, oviposition and development. Funct Ecol. 2012;26:1365–2435.
Google Scholar 
Ganter PF. Yeast and invertebrate associations. In: Gábor P, Carlos R, editors. Biodiversity and ecophysiology of yeasts. Berlin, Heidelberg: Springer; 2006. pp 303–70.Anagnostou C, Legrand EA, Rohlfs M. Friendly food for fitter flies?—Influence of dietary microbial species on food choice and parasitoid resistance in Drosophila. Oikos. 2010;119:533–41.
Google Scholar 
Günther CS, Knight SJ, Jones R, Goddard MR. Are Drosophila preferences for yeasts stable or contextual? Ecol Evol. 2019;9:8075–86.
Google Scholar 
Luo Y, Johnson JC, Chakraborty TS, Piontkowski A, Gendron CM, Pletcher SD. Yeast volatiles double starvation survival in Drosophila. Sci Adv. 2021;7:eabf8896.CAS 

Google Scholar 
Fogleman S. Coadaptation of Drosophila and yeasts in their natural habitat. J Chem Ecol. 1986;12:1037–55.
Google Scholar 
Droby S, Eick A, Macarisin D, Cohen L, Rafael G, Stange R, et al. Role of citrus volatiles in host recognition, germination and growth of Penicillium digitatum and Penicillium italicum. Postharvest Biol Tec. 2008;49:386–96.CAS 

Google Scholar 
Stensmyr MC, Dweck HK, Farhan A, Ibba I, Strutz A, Mukunda L, et al. A conserved dedicated olfactory circuit for detecting harmful microbes in Drosophila. Cell. 2012;151:1345–57.CAS 

Google Scholar 
Melo N, Wolff GH, Costa-da-Silva AL, Arribas R, Triana MF, Gugger M, et al. Geosmin attracts Aedes aegypti mosquitoes to oviposition sites. Curr Biol. 2020;30:127–34.CAS 

Google Scholar 
Wei DD, He W, Lang N, Miao ZQ, Xiao LF, Dou W, et al. Recent research status of Bactrocera dorsalis: Insights from resistance mechanisms and population structure. Arch Insect Biochem. 2019;102:e21601.CAS 

Google Scholar 
Han P, Wang X, Niu CY, Dong YC, Zhu JQ, Desneux N. Population dynamics, phenology, and overwintering of Bactrocera dorsalis (Diptera: Tephritidae) in Hubei Province, China. J Pest Sci. 2011;84:289–95.
Google Scholar 
Duyck PF, David P, Quilici S. A review of relationships between interspecific competition and invasions in fruit flies (Diptera: Tephritidae). Ecol Entomol. 2004;29:511–20.
Google Scholar 
Wen T, Zheng L, Dong S, Gong Z, Sang M, Long X, et al. Rapid detection and classification of citrus fruits infestation by Bactrocera dorsalis (Hendel) based on electronic nose. Postharvest Biol Tec. 2019;147:156–65.
Google Scholar 
Li X, Yang H, Wang T, Wang J, Wei H. Life history and adult dynamics of Bactrocera dorsalis in the citrus orchard of Nanchang, a subtropical area from China: implications for a control timeline. ScienceAsia. 2019;45:212–20.
Google Scholar 
Chalupowicz D, Veltman B, Droby S, Eltzov E. Evaluating the use of biosensors for monitoring of Penicillium digitatum infection in citrus fruit. Sens Actuat B-Chem. 2020;311:127896.CAS 

Google Scholar 
Turlings TC, Lengwiler UB, Bernasconi ML, Wechsler D. Timing of induced volatile emissions in maize seedlings. Planta. 1998;207:146–52.CAS 

Google Scholar 
Wang B, Dong W, Li H, D’Onofrio C, Bai P, Chen R, et al. Molecular basis of (E)-β-farnesene-mediated aphid location in the predator Eupeodes corollae. Curr Biol. 2022;32:951–62.CAS 

Google Scholar 
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. Methods. 2001;25:402–8.CAS 

Google Scholar 
Cellar NA, De Nison JE, Seipelt CT, Twohig M, Burgess JA. Title of subordinate document. In: Dramatic improvements in assay reproducibility for water-soluble vitamins using ACQUITY UPLC and the Ultra-Sensitive Xevo TQ-S Mass Spectrometer. 2013. https://www.waters.com/webassets/cms/library/docs/720004690en.pdf.Ren FR, Sun X, Wang TY, Yan JY, Yao YL, Li CQ, et al. Pantothenate mediates the coordination of whitefly and symbiont fitness. ISME J. 2021;15:1655–67.CAS 

Google Scholar 
Batta YA. Quantitative postharvest contamination and transmission of Penicillium expansum (Link) conidia to nectarine and pear fruit by Drosophila melanogaster (Meig.) adults. Postharvest Biol Tec. 2006;40:190–6.
Google Scholar 
Rohlfs M. Clash of kingdoms or why Drosophila larvae positively respond to fungal competitors. Front Zool. 2005;2:2.
Google Scholar 
Becher PG, Bengtsson M, Hansson BS, Witzgall P. Flying the fly: long-range flight behavior of Drosophila melanogaster to attractive odors. J Chem Ecol. 2010;36:599–607.CAS 

Google Scholar 
Dionigi C, Ahten T, Wartelle L. Effects of several metals on spore, biomass, and geosmin production by Streptomyces tendae and Penicillium expansum. J Ind Microbiol Biot. 1996;17:84–88.CAS 

Google Scholar 
Jin S, Zhou X, Gu F, Zhong G, Yi X. Olfactory plasticity: variation in the expression of chemosensory receptors in Bactrocera dorsalis in different physiological states. Front Physiol. 2017;8:672.
Google Scholar 
Li H, Ren L, Xie M, Gao Y, He M, Hassan B, et al. Egg-surface bacteria are indirectly associated with oviposition aversion in Bactrocera dorsalis. Curr Biol. 2020;30:4432–40.CAS 

Google Scholar 
Liu Y, Cui Z, Si P, Liu Y, Zhou Q, Wang G. Characterization of a specific odorant receptor for linalool in the Chinese citrus fly Bactrocera minax (Diptera: Tephritidae). Insect Biochem Molec. 2020;122:103389.CAS 

Google Scholar 
Ju JF, Bing XL, Zhao DS, Guo Y, Hong XY. Wolbachia supplement biotin and riboflavin to enhance reproduction in planthoppers. ISME J. 2019;14:1–12.
Google Scholar 
Liu F, Wickham JD, Cao Q, Lu M, Sun J. An invasive beetle–fungus complex is maintained by fungal nutritional-compensation mediated by bacterial volatiles. ISME J. 2020;14:2829–42.CAS 

Google Scholar 
Douglas AE. The B vitamin nutrition of insects: the contributions of diet, microbiome and horizontally acquired genes. Curr Opin Insect Sci. 2017;23:65–69.
Google Scholar 
Honda K, Ômura H, Hayashi N, Abe F, Yamauchi T. Conduritols as oviposition stimulants for the danaid butterfly, Parantica sita, identified from a host plant, Marsdenia tomentosa. J Chem Ecol. 2004;30:2285–96.CAS 

Google Scholar 
Soldano A, Alpizar YA, Boonen B, Franco L, Lopez-Requena A, Liu G, et al. Gustatory-mediated avoidance of bacterial lipopolysaccharides via TRPA1 activation in Drosophila. Elife. 2016;5:e13133.
Google Scholar 
Hussain A, Üçpunar HK, Zhang M, Loschek LF, Grunwald Kadow IC. Neuropeptides modulate female chemosensory processing upon mating in Drosophila. PLoS Biol. 2016;14:e1002455.
Google Scholar 
Stötefeld L, Holighaus G, Schütz S, Rohlfs M. Volatile-mediated location of mutualist host and toxic non-host microfungi by Drosophila larvae. Chemoecology. 2015;5:271–83.
Google Scholar 
Gou B, Liu Y, Guntur A, Stern U, Yang HC. Mechanosensitive neurons on the internal reproductive tract contribute to egg-laying-induced acetic acid attraction in Drosophila. Cell Rep. 2014;9:522–30.CAS 

Google Scholar 
Mezzera C, Brotas M, Gaspar M, Pavlou HJ, Goodwin SF, Vasconcelos ML. Ovipositor extrusion promotes the transition from courtship to copulation and signals female acceptance in Drosophila melanogaster. Curr Biol. 2020;30:3736–48.CAS 

Google Scholar 
Teimoori-Boghsani Y, Ganjeali A, Cernava T, Müller H, Asili J, Berg G. Endophytic fungi of native Salvia abrotanoides plants reveal high taxonomic diversity and unique profiles of secondary metabolites. Front Microbiol. 2020;10:3013–20.
Google Scholar 
Holden JT, Furman C, Snell EE. D-alanine and the vitamin B6 content of microorganisms. J Biol Chem. 1949;178:789–97.CAS 

Google Scholar 
Michalkova V, Benoit JB, Weiss BL, Attardo GM, Aksoy S. Vitamin B6 generated by obligate symbionts is critical for maintaining proline homeostasis and fecundity in tsetse flies. Appl Environ Micro. 2014;80:5844–53.
Google Scholar 
Ren FR, Sun X, Wang TY, Yao YL, Huang YZ, Zhang X, et al. Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits. ISME J. 2020;14:2542–53.CAS 

Google Scholar 
Salem H, Bauer E, Strauss AS, Vogel H, Marz M, Kaltenpoth M. Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host. Proc Biol Sci. 2014;281:20141838.
Google Scholar  More

Meredith M, Sommerkorn M, Cassotta S, Derksen C, Ekaykin A, Hollowed A. IPCC special report on the ocean and cryosphere in a changing climate In: Pörtner H-O, Roberts D, Masson-Delmotte V, Zhai P, Tignor M, Poloczanska Eea, editors. 2022; chapter 3: https://doi.org/10.1017/9781009157964 (in press).Rozema PD, Venables HJ, van de Poll WH, Clarke A, Meredith MP, Buma AGJ. Interannual variability in phytoplankton biomass and species composition in northern Marguerite Bay (West Antarctic Peninsula) is governed by both winter sea ice cover and summer stratification. Limnol Oceanogr. 2017;62:235–52.Article 

Google Scholar 
Venables HJ, Clarke A, Meredith MP. Wintertime controls on summer stratification and productivity at the western Antarctic Peninsula. Limnol Oceanogr. 2013;58:1035–47.Article 

Google Scholar 
Barnes DKA, Souster T. Reduced survival of Antarctic benthos linked to climate-induced iceberg scouring. Nat Clim Change. 2011;1:365–8.Article 

Google Scholar 
Grange L, Tyler P, Peck L, Cornelius N. Long-term interannual cycles of the gametogenic ecology of the Antarctic brittle star Ophionotus victoriae. Mar Ecol Prog Ser. 2004;278:141–55.Article 

Google Scholar 
Schratzberger M, Ingels J. Meiofauna matters: The roles of meiofauna in benthic ecosystems. J Exp Mar Biol Ecol. 2018;502:12–25.Article 

Google Scholar 
Mayor D, Thornton B, Jenkins H, Felgate S. Microbiota: the living foundation. In: Beninger P, editor. Mudflat ecology. Switzerland AG: Springer Nature 2018. p. 43–61.Fonseca VG, Sinniger F, Gaspar JM, Quince C, Creer S, Power DM, et al. Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach. Sci Rep. 2017;7:6094.CAS 
Article 

Google Scholar 
Vause BJ, Morley SA, Fonseca VG, Jazdzewska A, Ashton GV, Barnes DKA, et al. Spatial and temporal dynamics of Antarctic shallow soft-bottom benthic communities: ecological drivers under climate change. BMC Ecol. 2019;19:27.Article 

Google Scholar 
Danovaro R, Scopa M, Gambi C, Fraschetti S. Trophic importance of subtidal metazoan meiofauna: evidence from in situ exclusion experiments on soft and rocky substrates. Mar Biol. 2007;152:339–50.Article 

Google Scholar 
Watzin MC. The effects of meiofauna on settling macrofauna: meiofauna may structure macrofaunal communities. Oecologia. 1983;59:163–6.Article 

Google Scholar 
Schmidt JL, Deming JW, Jumars PA, Keil RG. Constancy of bacterial abundance in surficial marine sediments. Limnol Oceanogr. 1998;43:976–82.Article 

Google Scholar 
Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA. 1998;95:6578–83.CAS 
Article 

Google Scholar 
Burdige DJ. Preservation of organic matter in marine sediments: controls, mechanisms, and an imbalance in sediment organic carbon budgets? Chem Rev. 2007;107:467–85.CAS 
Article 

Google Scholar 
Zou K, Thébault E, Lacroix G, Barot S. Interactions between the green and brown food web determine ecosystem functioning. Funct Ecol. 2016;30:1454–65.Article 

Google Scholar 
Anderson TR, Pond DW, Mayor DJ. The role of microbes in the nutrition of detritivorous invertebrates: a stoichiometric analysis. Front Microbiol. 2016;7:2113.
Google Scholar 
Lacoste E, Piot A, Archambault P, McKindsey CW, Nozais C. Bioturbation activity of three macrofaunal species and the presence of meiofauna affect the abundance and composition of benthic bacterial communities. Mar Environ Res. 2018;136:62–70.CAS 
Article 

Google Scholar 
Bonaglia S, Nascimento FJ, Bartoli M, Klawonn I, Bruchert V. Meiofauna increases bacterial denitrification in marine sediments. Nat Commun. 2014;5:5133.CAS 
Article 

Google Scholar 
Riemann F, Helmke E. Symbiotic relations of sediment-agglutinating nematodes and bacteria in detrital habitats: the enzyme-sharing concept. Mar Ecol. 2002;23:93–113.CAS 
Article 

Google Scholar 
dos Santos GAP, Derycke S, Fonseca-Genevois VG, Coelho LCBB, Correia MTS, Moens T. Differential effects of food availability on population growth and fitness of three species of estuarine, bacterial-feeding nematodes. J Exp Mar Biol Ecol. 2008;355:27–40.Article 

Google Scholar 
Zeppilli D, Sarrazin J, Leduc D, Arbizu PM, Fontaneto D, Fontanier C, et al. Is the meiofauna a good indicator for climate change and anthropogenic impacts? Mar Biodivers. 2015;45:505–35.Article 

Google Scholar 
Moens T, Beninger PG. Meiofauna: an inconspicuous but important player in Mudflat ecology. In: Beninger P, editor. Mudflat ecology aquatic ecology series. 7. Switzerland: Springer; 2018.Webb AL, Hughes KA, Grand MM, Lohan MC, Peck LS. Sources of elevated heavy metal concentrations in sediments and benthic marine invertebrates of the western Antarctic Peninsula. Sci Total Environ. 2020;698:134268.CAS 
Article 

Google Scholar 
Brown KM, Fraser KP, Barnes DK, Peck LS. Links between the structure of an Antarctic shallow-water community and ice-scour frequency. Oecologia. 2004;141:121–9.Article 

Google Scholar 
Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Breiner H-W, et al. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol. 2010;19:21–31.CAS 
Article 

Google Scholar 
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6:1621–4.CAS 
Article 

Google Scholar 
Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N, Ranwez V, et al. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front Zool. 2013;10:34.Article 

Google Scholar 
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10–2.Article 

Google Scholar 
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.CAS 
Article 

Google Scholar 
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinform. 2009;10:421.Article 

Google Scholar 
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8:e61217.CAS 
Article 

Google Scholar 
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.CAS 
Article 

Google Scholar 
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res. 2005;33:D34–8.CAS 
Article 

Google Scholar 
Wentworth CK. A scale of grade and class terms for clastic sediments. J Geol. 1922;30:377–92.Article 

Google Scholar 
Dean WE. Determination of carbonate and organic matter in calcareous sediments and sedimentary rocks by loss on ignition; comparison with other methods. J Sediment Res. 1974;44:242–8.CAS 

Google Scholar 
Tatzber M, Stemmer M, Spiegel H, Katzlberger C, Haberhauer G, Gerzabek MH. An alternative method to measure carbonate in soils by FT-IR spectroscopy. Environ Chem Lett. 2007;5:9–12.CAS 
Article 

Google Scholar 
Hsieh CH, Reiss CS, Hunter JR, Beddington JR, May RM, Sugihara G. Fishing elevates variability in the abundance of exploited species. Nature. 2006;443:859–62.CAS 
Article 

Google Scholar 
Elbrecht V, Braukmann TWA, Ivanova NV, Prosser SWJ, Hajibabaei M, Wright M, et al. Validation of COI metabarcoding primers for terrestrial arthropods. Peer J. 2019;7:e7745–e.Article 

Google Scholar 
Kirse A, Bourlat SJ, Langen K, Fonseca VG. Unearthing the potential of Soil eDNA metabarcoding—towards best practice advice for invertebrate biodiversity assessment. Front. Ecol. Evol. 2021;9:630560.Article 

Google Scholar 
Zhang GK, Chain FJJ, Abbott CL, Cristescu ME. Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities. Evolut Appl. 2018;11:1901–14.CAS 
Article 

Google Scholar 
Marquina D, Andersson AF, Ronquist F. New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods. Mol Ecol Resour. 2019;19:90–104.CAS 
Article 

Google Scholar 
Leasi F, Sevigny JL, Laflamme EM, Artois T, Curini-Galletti M, de Jesus Navarrete A, et al. Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach. Commun Biol. 2018;1:112.Article 

Google Scholar 
Giebner H, Langen K, Bourlat SJ, Kukowka S, Mayer C, Astrin JJ, et al. Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes. Mol Ecol Resour. 2020;20:1333–45.CAS 
Article 

Google Scholar 
Vanhove S, Lee HJ, Beghyn M, Gansbeke DV, Brockington S, Vincx M. The Metazoan Meiofauna in its biogeochemical environment: the case of an Antarctic coastal sediment. J Mar Biol Assoc UK. 1998;78:411–34.Article 

Google Scholar 
Pasotti F, Saravia LA, De Troch M, Tarantelli MS, Sahade R, Vanreusel A. Benthic Trophic Interactions in an Antarctic Shallow Water Ecosystem Affected by Recent Glacier Retreat. PLoS ONE. 2015;10:e0141742.Article 

Google Scholar 
Griffiths JR, Kadin M, Nascimento FJA, Tamelander T, Tornroos A, Bonaglia S, et al. The importance of benthic-pelagic coupling for marine ecosystem functioning in a changing world. Global Change Biology. 2017;23:2179–96.Article 

Google Scholar 
Virta L, Gammal J, Järnström M, Bernard G, Soininen J, Norkko J, et al. The diversity of benthic diatoms affects ecosystem productivity in heterogeneous coastal environments. Ecology. 2019;100:e02765.Article 

Google Scholar 
Malviya S, Scalco E, Audic S, Vincent F, Veluchamy A, Poulain J, et al. Insights into global diatom distribution and diversity in the world’s ocean. Proc Natl Acad Sci USA. 2016;113:E1516–25.CAS 
Article 

Google Scholar 
Forster D, Dunthorn M, Mahe F, Dolan JR, Audic S, Bass D, et al. Benthic protists: the under-charted majority. Fems Microbiol Ecol. 2016;92:fiw120.Article 

Google Scholar 
Fonseca VG, Carvalho GR, Nichols B, Quince C, Johnson HF, Neill SP, et al. Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes. Glob Ecol Biogeogr. 2014;23:1293–302.Article 

Google Scholar 
O’Malley MA. The nineteenth century roots of ‘everything is everywhere’. Nat Rev Microbiol. 2007;5:647–51.Article 

Google Scholar 
Pasotti F, Manini E, Giovannelli D, Wölfl A-C, Monien D, Verleyen E, et al. Antarctic shallow water benthos in an area of recent rapid glacier retreat. Mar Ecol. 2015;36:716–33.Article 

Google Scholar 
Molari M, Janssen F, Vonnahme TR, Wenzhöfer F, Boetius A. The contribution of microbial communities in polymetallic nodules to the diversity of the deep-sea microbiome of the Peru Basin (4130–4198 m depth). Biogeosciences. 2020;17:3203–22.CAS 
Article 

Google Scholar 
Signori CN, Thomas F, Enrich-Prast A, Pollery RCG, Sievert SM. Microbial diversity and community structure across environmental gradients in Bransfield Strait, Western Antarctic Peninsula. Front Microbiol. 2014;5:647.Article 

Google Scholar 
Ozturk RC, Feyzioglu AM, Altinok I. Prokaryotic community and diversity in coastal surface waters along the Western Antarctic Peninsula. Pol Sci. 2021;31:100764.Article 

Google Scholar 
Ghiglione JF, Murray AE. Pronounced summer to winter differences and higher wintertime richness in coastal Antarctic marine bacterioplankton. Environ Microbiol. 2012;14:617–29.CAS 
Article 

Google Scholar 
Luria CM, Ducklow HW, Amaral-Zettler LA. Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the western Antarctic Peninsula. Aquat Microbial Ecol. 2014;73:107–21.Article 

Google Scholar 
Cao S, He J, Zhang F, Lin L, Gao Y, Zhou Q. Diversity and community structure of bacterioplankton in surface waters off the northern tip of the Antarctic Peninsula. Pol Res. 2019;38:3491.Article 

Google Scholar 
Walsh EA, Kirkpatrick JB, Rutherford SD, Smith DC, Sogin M, D’Hondt S. Bacterial diversity and community composition from seasurface to subseafloor. ISME J. 2016;10:979–89.Article 

Google Scholar 
Kiko R, Werner I, Wittmann A. Osmotic and ionic regulation in response to salinity variations and cold resistance in the Arctic under-ice amphipod Apherusa glacialis. Pol Biol. 2009;32:393–8.Article 

Google Scholar 
Zeppilli D, Leduc D, Fontanier C, Fontaneto D, Fuchs S, Gooday AJ, et al. Characteristics of meiofauna in extreme marine ecosystems: a review. Mar Biodivers. 2018;48:35–71.Article 

Google Scholar 
Arnosti C, Joergensen BB, Sagemann J, Thamdrup B. Temperature dependence of microbial degradation of organic matter in marine sediments: polysaccharide hydrolysis, oxygen consumption, and sulfate reduction. Mar Ecol Prog Ser. 1998;165:59–70.CAS 
Article 

Google Scholar 
Fabiano M, Danovaro R. Enzymatic activity, bacterial distribution, and organic matter composition in sediments of the ross sea (Antarctica). Appl Environ Microbiol. 1998;64:3838–45.CAS 
Article 

Google Scholar 
Kujawinski EB, Longnecker K, Barott KL, Weber RJM, Kido Soule, MC. Microbial community structure affects marine dissolved organic matter composition. Front Mar Sci. 2016;3:45.Article 

Google Scholar 
Barrett JE, Virginia RA, Hopkins DW, Aislabie J, Bargagli R, Bockheim JG, et al. Terrestrial ecosystem processes of Victoria Land, Antarctica. Soil Biol Biochem. 2006;38:3019–34.CAS 
Article 

Google Scholar 
Ganzert L, Lipski A, Hubberten H-W, Wagner D. The impact of different soil parameters on the community structure of dominant bacteria from nine different soils located on Livingston Island, South Shetland Archipelago, Antarctica. Fems Microbiol Ecol. 2011;76:476–91.CAS 
Article 

Google Scholar 
Rusch A, Huettel M, Reimers CE, Taghon GL, Fuller CM. Activity and distribution of bacterial populations in Middle Atlantic Bight shelf sands. Fems Microbiol Ecol. 2003;44:89–100.CAS 
Article 

Google Scholar 
Hemkemeyer M, Dohrmann AB, Christensen BT, Tebbe CC. Bacterial preferences for specific soil particle size fractions revealed by community analyses. Front Microbiol. 2018;9:149.Article 

Google Scholar 
Giere O. Meiobenthology: the microscopic motile fauna of aquatic sediments. 2nd ed: Springer-Verlag Berlin Heidelberg; 2009. 527 p.Fonseca VG, Carvalho GR, Sung W, Johnson HF, Power DM, Neill SP, et al. Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat Commun. 2010;1:98.Article 

Google Scholar 
Pitcher RC, Lawton P, Ellis N, Smith SJ, Incze LS, Wei C-L, et al. Exploring the role of environmental variables in shaping patterns of seabed biodiversity composition in regional-scale ecosystems. J Appl Ecol. 2012;49:670–9.Article 

Google Scholar 
Rose A, Ingels J, Raes M, Vanreusel A, Arbizu PM. Long-term iceshelf-covered meiobenthic communities of the Antarctic continental shelf resemble those of the deep sea. Heidelberg: Springer; 2014. 743–62 p.Gonçalves-Araujo R, de Souza MS, Tavano VM, Garcia CAE. Influence of oceanographic features on spatial and interannual variability of phytoplankton in the Bransfield Strait, Antarctica. J Mar Syst. 2015;142:1–15.Article 

Google Scholar 
Learman DR, Henson MW, Thrash JC, Temperton B, Brannock PM, Santos SR, et al. Biogeochemical and microbial variation across 5500 km of Antarctic surface sediment implicates organic matter as a driver of benthic community structure. Front Microbiol. 2016;7:284.Article 

Google Scholar 
Ghiglione JF, Galand PE, Pommier T, Pedros-Alio C, Maas EW, Bakker K, et al. Pole-to-pole biogeography of surface and deep marine bacterial communities. Proc Natl Acad Sci USA. 2012;109:17633–8.CAS 
Article 

Google Scholar 
Rosli N, Leduc D, Rowden A, Probert P. Review of recent trends in ecological studies of deep-sea meiofauna, with focus on patterns and processes at small to regional spatial scales. Mar Biodivers. 2017;48:13–34.Article 

Google Scholar 
Ruff SE, Probandt D, Zinkann A-C, Iversen M, Klaas C, Schwabe L, et al. Indications for algae-degrading benthic microbial communities in deep-sea sediments along the Antarctic Polar Front. Deep Sea Res Part II: Top Stud Oceanogr. 2014;108:6–16.Article 

Google Scholar 
El-Serehy HA, Al-Rasheid KA, Al-Misned FA, Al-Talasat AA, Gewik MM. Microbial-meiofaunal interrelationships in coastal sediments of the Red Sea. Saudi J Biol Sci. 2016;23:327–34.CAS 
Article 

Google Scholar 
Danovaro R, Company JB, Corinaldesi C, D’Onghia G, Galil B, Gambi C, et al. Deep-sea biodiversity in the Mediterranean Sea: the known, the unknown, and the unknowable. PLoS ONE. 2010;5:e11832.Article 

Google Scholar 
Mussmann M, Pjevac P, Kruger K, Dyksma S. Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments. ISME J. 2017;11:1276–81.CAS 
Article 

Google Scholar 
Hinger I, Pelikan C, Mußmann M. Role of the ubiquitous bacterial family Woeseiaceae for N2O production in marine sediments. Geophys Res Abstracts. 2019;21:17441.
Google Scholar 
Hoffmann K, Bienhold C, Buttigieg PL, Knittel K, Laso-Pérez R, Rapp JZ, et al. Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities. ISME J. 2020;14:1042–56.CAS 
Article 

Google Scholar 
Mare MF. A study of a marine benthic community with special reference to the microorganisms. J Mar Biol Assoc UK. 1942;25:517–54.Article 

Google Scholar 
Bott TL, Borchardt MA. Grazing of protozoa, bacteria, and diatoms by Meiofauna in lotic epibenthic communities. J North Am Bentholog Soc. 1999;18:499–513.Article 

Google Scholar 
Griffiths HJ. Antarctic marine biodiversity-what do we know about the distribution of life in the Southern Ocean? PLoS ONE. 2010;5:e11683.Article 

Google Scholar 
Convey P, Chown SL, Clarke A, Barnes DKA, Bokhorst S, Cummings V, et al. The spatial structure of Antarctic biodiversity. Ecol Monogr. 2014;84:203–44.Article 

Google Scholar 
Li L, Ma ZS. Species sorting and neutral theory analyses reveal archaeal and bacterial communities are assembled differently in hot springs. Front Bioeng Biotechnol. 2020;8:464.Article 

Google Scholar 
Lee JE, Buckley HL, Etienne RS, Lear G. Both species sorting and neutral processes drive assembly of bacterial communities in aquatic microcosms. Fems Microbiol Ecol. 2013;86:288–302.CAS 
Article 

Google Scholar 
Gansfort B, Fontaneto D, Zhai M. Meiofauna as a model to test paradigms of ecological metacommunity theory. Hydrobiologia. 2020;847:2645–63.Article 

Google Scholar 
Convey P, Peck LS. Antarctic environmental change and biological responses. Sci Adv. 2019;5:eaaz0888.CAS 
Article 

Google Scholar  More

Brown MV, Philip GK, Bunge JA, Smith MC, Bissett A, Lauro FM, et al. Microbial community structure in the North Pacific ocean. ISME J. 2009;3:1374–86.CAS 
Article 

Google Scholar 
Chénard C, Wijaya W, Vaulot D, dos Santos AL, Martin P, Kaur A, et al. Temporal and spatial dynamics of Bacteria, Archaea and protists in equatorial coastal waters. Sci Rep. 2019;9:1–13.Article 

Google Scholar 
Yeh YC, McNichol J, Needham DM, Fichot EB, Berdjeb L, Fuhrman JA. Comprehensive single‐PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S. Environ Microbiol. 2021;23:2340–3250.Article 

Google Scholar 
Needham DM, Fuhrman JA. Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom. Nat. Microbiol. 2016;1:16005.CAS 
Article 

Google Scholar 
Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 2016;18:1403–14.CAS 
Article 

Google Scholar 
Needham DM, Fichot EB, Wang E, Berdjeb L, Cram JA, Fichot CG, et al. Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling. ISME J. 2018;12:2417.CAS 
Article 

Google Scholar 
Steinberg DK, Carlson CA, Bates NR, Johnson RJ, Michaels AF, Knap AH. Overview of the US JGOFS Bermuda Atlantic Time-series Study (BATS): a decade-scale look at ocean biology and biogeochemistry. Deep Sea Res Part II Top Stud Oceanogr. 2001;48:1405–47.CAS 
Article 

Google Scholar 
Karl DM, Church MJ. Microbial oceanography and the Hawaii Ocean Time-series programme. Nat Rev Microbiol. 2014;12:699–713.CAS 
Article 

Google Scholar 
Mestre M, Höfer J, Sala MM, Gasol JM. Seasonal variation of bacterial diversity along the marine particulate matter continuum. Front Microbiol. 2020;11:1590.Article 

Google Scholar 
Cram JA, Chow C-ET, Sachdeva R, Needham DM, Parada AE, Steele JA, et al. Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. ISME J. 2015;9:563–80.Article 

Google Scholar 
Berelson WM. The flushing of two deep‐sea basins, southern California borderland. Limnol Oceanogr. 1991;36:1150–66.CAS 
Article 

Google Scholar 
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.CAS 
Article 

Google Scholar 
Traving SJ, Kellogg CT, Ross T, McLaughlin R, Kieft B, Ho GY, et al. Prokaryotic responses to a warm temperature anomaly in northeast subarctic Pacific waters. Commun Biology. 2021;4:1–12.Article 

Google Scholar 
Butler TM, Wilhelm A-C, Dwyer AC, Webb PN, Baldwin AL, Techtmann SM. Microbial community dynamics during lake ice freezing. Scient Rep. 2019;9:1–11.
Google Scholar 
LeBrun ES, King RS, Back JA, Kang S. Microbial community structure and function decoupling across a phosphorus gradient in streams. Microb Ecol. 2018;75:64–73.CAS 
Article 

Google Scholar 
McNichol J, Berube PM, Biller SJ, Fuhrman JA. Evaluating and improving small subunit rRNA PCR primer coverage for bacteria, archaea, and eukaryotes using metagenomes from global ocean surveys. Msystems. 2021;6:e00565–21.CAS 
Article 

Google Scholar 
De Bie T, De Meester L, Brendonck L, Martens K, Goddeeris B, Ercken D, et al. Body size and dispersal mode as key traits determining metacommunity structure of aquatic organisms. Ecol Lett. 2012;15:740–7.Article 

Google Scholar 
Soininen J, Korhonen JJ, Karhu J, Vetterli A. Disentangling the spatial patterns in community composition of prokaryotic and eukaryotic lake plankton. Limnol. Oceanogr. 2011;56:508–20.Article 

Google Scholar 
Wu W, Lu H-P, Sastri A, Yeh Y-C, Gong G-C, Chou W-C, et al. Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities. ISME J. 2018;12:485–94.Article 

Google Scholar 
Kraemer S, Ramachandran A, Colatriano D, Lovejoy C, Walsh DA. Diversity and biogeography of SAR11 bacteria from the Arctic Ocean. ISME J. 2020;14:79–90.Article 

Google Scholar 
Tsementzi D, Wu J, Deutsch S, Nath S, Rodriguez-R LM, Burns AS, et al. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature. 2016;536:179–83.CAS 
Article 

Google Scholar 
Brown MV, Lauro FM, DeMaere MZ, Muir L, Wilkins D, Thomas T, et al. Global biogeography of SAR11 marine bacteria. Mol Syst Biol. 2012;8:595.Article 

Google Scholar 
Giovannoni SJ. SAR11 bacteria: the most abundant plankton in the oceans. Ann Rev Mar Sci. 2017;9:231–55.Article 

Google Scholar 
Thrash JC, Temperton B, Swan BK, Landry ZC, Woyke T, DeLong EF, et al. Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. ISME J. 2014;8:1440–51.Article 

Google Scholar 
Fernández-Gomez B, Richter M, Schüler M, Pinhassi J, Acinas SG, González JM, et al. Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J. 2013;7:1026–37.Article 

Google Scholar 
Countway PD, Vigil PD, Schnetzer A, Moorthi SD, Caron DA. Seasonal analysis of protistan community structure and diversity at the USC Microbial Observatory (San Pedro Channel, North Pacific Ocean). Limnol Oceanogr. 2010;55:2381–96.Article 

Google Scholar 
Kim DY, Countway PD, Jones AC, Schnetzer A, Yamashita W, Tung C, et al. Monthly to interannual variability of microbial eukaryote assemblages at four depths in the eastern North Pacific. ISME J. 2014;8:515–30.Article 

Google Scholar 
Parris DJ, Ganesh S, Edgcomb VP, DeLong EF, Stewart FJ. Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile. Front Microbiol. 2014;5:543.Article 

Google Scholar 
Orsi W, Song YC, Hallam S, Edgcomb V. Effect of oxygen minimum zone formation on communities of marine protists. ISME J. 2012;6:1586–601.CAS 
Article 

Google Scholar 
Leibold MA, Holyoak M, Mouquet N, Amarasekare P, Chase JM, Hoopes MF, et al. The metacommunity concept: a framework for multi‐scale community ecology. Ecol Lett. 2004;7:601–13.Article 

Google Scholar 
Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV, Naeem S. Annually reoccurring bacterial communities are predictable from ocean conditions. Proc Natl Acad Sci USA. 2006;103:13104–9.CAS 
Article 

Google Scholar 
Chow C-ET, Sachdeva R, Cram JA, Steele JA, Needham DM, Patel A, et al. Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight. ISME J. 2013;7:2259–73.CAS 
Article 

Google Scholar 
Parada AE, Fuhrman JA. Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor. ISME J. 2017;11:2510–25.Article 

Google Scholar 
Mestre M, Ruiz-González C, Logares R, Duarte CM, Gasol JM, Sala MM. Sinking particles promote vertical connectivity in the ocean microbiome. Proc Natl Acad Sci USA. 2018;115:E6799–E807.CAS 
Article 

Google Scholar 
Mestre M, Ferrera I, Borrull E, Ortega‐Retuerta E, Mbedi S, Grossart HP, et al. Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum. Mol Ecol. 2017;26:6827–40.CAS 
Article 

Google Scholar 
Wilson B, Müller O, Nordmann E-L, Seuthe L, Bratbak G, Øvreås L. Changes in marine prokaryote composition with season and depth over an Arctic polar year. Front Mar Sci. 2017;4:95.
Google Scholar 
Treusch AH, Vergin KL, Finlay LA, Donatz MG, Burton RM, Carlson CA, et al. Seasonality and vertical structure of microbial communities in an ocean gyre. ISME J. 2009;3:1148–63.Article 

Google Scholar 
Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-Devine MC, Huse SM, Welch DBM, et al. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE. 2011;6:e24570.CAS 
Article 

Google Scholar 
DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard N-U, et al. Community genomics among stratified microbial assemblages in the ocean’s interior. Science. 2006;311:496–503.CAS 
Article 

Google Scholar 
Agogué H, Lamy D, Neal PR, Sogin ML, Herndl GJ. Water mass‐specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing. Mol. Ecol. 2011;20:258–74.Article 

Google Scholar 
Walsh EA, Kirkpatrick JB, Rutherford SD, Smith DC, Sogin M, D’Hondt S. Bacterial diversity and community composition from seasurface to subseafloor. ISME J. 2016;10:979–89.Article 

Google Scholar 
Reji L, Tolar BB, Chavez FP, Francis CA. Depth-differentiation and seasonality of planktonic microbial assemblages in the Monterey Bay upwelling system. Front Microbiol. 2020;11:1075.Article 

Google Scholar 
Milici M, Vital M, Tomasch J, Badewien TH, Giebel HA, Plumeier I, et al. Diversity and community composition of particle‐associated and free‐living bacteria in mesopelagic and bathypelagic Southern Ocean water masses: Evidence of dispersal limitation in the Bransfield Strait. Limnol Oceanogr. 2017;62:1080–95.Article 

Google Scholar 
Crespo BG, Pommier T, Fernández‐Gómez B, Pedrós‐Alió C. Taxonomic composition of the particle‐attached and free‐living bacterial assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of the 16S rRNA. Microbiologyopen. 2013;2:541–52.CAS 
Article 

Google Scholar 
Ganesh S, Parris DJ, DeLong EF, Stewart FJ. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. ISME J. 2014;8:187–211.CAS 
Article 

Google Scholar 
Ghiglione J-F, Galand PE, Pommier T, Pedrós-Alió C, Maas EW, Bakker K, et al. Pole-to-pole biogeography of surface and deep marine bacterial communities. Proc Natl Acad Sci USA. 2012;109:17633–8.CAS 
Article 

Google Scholar 
Murillo AA, Ramírez-Flandes S, DeLong EF, Ulloa O. Enhanced metabolic versatility of planktonic sulfur-oxidizing γ-proteobacteria in an oxygen-deficient coastal ecosystem. Front Mar Sci. 2014;1:18.Article 

Google Scholar 
Hawley AK, Nobu MK, Wright JJ, Durno WE, Morgan-Lang C, Sage B, et al. Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients. Nat Commun. 2017;8:1–10.CAS 
Article 

Google Scholar 
Santoro AE, Buchwald C, McIlvin MR, Casciotti KL. Isotopic signature of N2O produced by marine ammonia-oxidizing archaea. Science. 2011;333:1282–5.CAS 
Article 

Google Scholar 
Aldunate M, De la Iglesia R, Bertagnolli AD, Ulloa O. Oxygen modulates bacterial community composition in the coastal upwelling waters off central Chile. Deep Sea Res Part II Top Stud Oceanogr. 2018;156:68–79.CAS 
Article 

Google Scholar 
Duret MT, Lampitt RS, Lam P. Prokaryotic niche partitioning between suspended and sinking marine particles. Environ Microbiol Rep. 2019;11:386–400.CAS 
Article 

Google Scholar 
Lindh MV, Sjöstedt J, Andersson AF, Baltar F, Hugerth LW, Lundin D, et al. Disentangling seasonal bacterioplankton population dynamics by high‐frequency sampling. Environ Microbiol. 2015;17:2459–76.Article 

Google Scholar 
Teeling H, Fuchs BM, Bennke CM, Krueger K, Chafee M, Kappelmann L, et al. Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms. elife. 2016;5:e11888.Article 

Google Scholar 
Buchan A, LeCleir GR, Gulvik CA, González JM. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat Rev Microbiol. 2014;12:686–98.CAS 
Article 

Google Scholar 
Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, Baptista D, et al. Genome streamlining in a cosmopolitan oceanic bacterium. Science. 2005;309:1242–5.CAS 
Article 

Google Scholar 
Cram JA, Xia LC, Needham DM, Sachdeva R, Sun F, Fuhrman JA. Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes. ISME J. 2015;9:2573–86.Article 

Google Scholar 
Salazar G, Cornejo‐Castillo FM, Borrull E, Díez‐Vives C, Lara E, Vaqué D, et al. Particle‐association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Mol Ecol. 2015;24:5692–706.Article 

Google Scholar 
Mohit V, Archambault P, Toupoint N, Lovejoy C. Phylogenetic differences in attached and free-living bacterial communities in a temperate coastal lagoon during summer, revealed via high-throughput 16S rRNA gene sequencing. Appl Environ Microbiol. 2014;80:2071–83.Article 

Google Scholar 
Rieck A, Herlemann DP, Jürgens K, Grossart H-P. Particle-associated differ from free-living bacteria in surface waters of the Baltic Sea. Front Microbiol. 2015;6:1297.Article 

Google Scholar 
Pachiadaki MG, Brown JM, Brown J, Bezuidt O, Berube PM, Biller SJ, et al. Charting the complexity of the marine microbiome through single-cell genomics. Cell. 2019;179:1623–35. e11.CAS 
Article 

Google Scholar 
Giner CR, Pernice MC, Balagué V, Duarte CM, Gasol JM, Logares R, et al. Marked changes in diversity and relative activity of picoeukaryotes with depth in the world ocean. ISME J. 2020;14:437–49.Article 

Google Scholar 
Countway PD, Gast RJ, Dennett MR, Savai P, Rose JM, Caron DA. Distinct protistan assemblages characterize the euphotic zone and deep sea (2500 m) of the western North Atlantic (Sargasso Sea and Gulf Stream). Environ Microbiol. 2007;9:1219–32.CAS 
Article 

Google Scholar 
Ollison GA, Hu SK, Mesrop LY, DeLong EF, Caron DA. Come rain or shine: depth not season shapes the active protistan community at station ALOHA in the North Pacific Subtropical Gyre. Deep Sea Res Part I Oceanogr Res Pap. 2021;170:103494.Article 

Google Scholar 
Schnetzer A, Moorthi SD, Countway PD, Gast RJ, Gilg IC, Caron DA. Depth matters: microbial eukaryote diversity and community structure in the eastern North Pacific revealed through environmental gene libraries. Deep Sea Res Part I Oceanogr Res Pap. 2011;58:16–26.Article 

Google Scholar 
Martin P, Allen JT, Cooper MJ, Johns DG, Lampitt RS, Sanders R, et al. Sedimentation of acantharian cysts in the Iceland Basin: strontium as a ballast for deep ocean particle flux, and implications for acantharian reproductive strategies. Limnol Oceanogr. 2010;55:604–14.CAS 
Article 

Google Scholar 
Lampitt R, Salter I, Johns D. Radiolaria: Major exporters of organic carbon to the deep ocean. Glob Biogeochem Cycle. 2009;23:GB1010.Article 

Google Scholar 
Skovgaard A, Massana R, Balague V, Saiz E. Phylogenetic position of the copepod-infesting parasite Syndinium turbo (Dinoflagellata, Syndinea). Protist. 2005;156:413–23.CAS 
Article 

Google Scholar 
Bachvaroff TR, Kim S, Guillou L, Delwiche CF, Coats DW. Molecular diversity of the syndinean genus Euduboscquella based on single-cell PCR analysis. Appl Environ Microbiol. 2012;78:334–45.CAS 
Article 

Google Scholar 
Guillou L, Viprey M, Chambouvet A, Welsh R, Kirkham A, Massana R, et al. Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ Microbiol. 2008;10:3349–65.CAS 
Article 

Google Scholar 
Berdjeb L, Parada A, Needham DM, Fuhrman JA. Short-term dynamics and interactions of marine protist communities during the spring–summer transition. ISME J. 2018;12:1907.Article 

Google Scholar 
Hu SK, Connell PE, Mesrop LY, Caron DA. A hard day’s night: diel shifts in microbial eukaryotic activity in the north pacific subtropical gyre. Front Mar Sci. 2018;5:351.Article 

Google Scholar 
Clarke LJ, Bestley S, Bissett A, Deagle BE. A globally distributed Syndiniales parasite dominates the Southern Ocean micro-eukaryote community near the sea-ice edge. ISME J. 2019;13:734–7.CAS 
Article 

Google Scholar 
De Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, et al. Eukaryotic plankton diversity in the sunlit ocean. Science. 2015;348:1261605.Article 

Google Scholar 
Pernice MC, Giner CR, Logares R, Perera-Bel J, Acinas SG, Duarte CM, et al. Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans. ISME J. 2016;10:945–58.Article 

Google Scholar 
Crutsinger GM, Collins MD, Fordyce JA, Gompert Z, Nice CC, Sanders NJ. Plant genotypic diversity predicts community structure and governs an ecosystem process. Science. 2006;313:966–8.CAS 
Article 

Google Scholar 
Hawkins BA, Porter EE. Does herbivore diversity depend on plant diversity? The case of California butterflies. Am Nat. 2003;161:40–9.Article 

Google Scholar 
Scherber C, Eisenhauer N, Weisser WW, Schmid B, Voigt W, Fischer M, et al. Bottom-up effects of plant diversity on multitrophic interactions in a biodiversity experiment. Nature. 2010;468:553–6.CAS 
Article 

Google Scholar 
Yang JW, Wu W, Chung C-C, Chiang K-P, Gong G-C, Hsieh C-h Predator and prey biodiversity relationship and its consequences on marine ecosystem functioning—interplay between nanoflagellates and bacterioplankton. ISME J. 2018;12:1532–42.Article 

Google Scholar 
Fuhrman JA, Comeau DE, Hagström Å, Chan AM. Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies. Appl Environ Microbiol. 1988;54:1426–9.CAS 
Article 

Google Scholar 
Lie AA, Kim DY, Schnetzer A, Caron DA. Small-scale temporal and spatial variations in protistan community composition at the San Pedro Ocean Time-series station off the coast of southern California. Aquat Microb Ecol. 2013;70:93–110.Article 

Google Scholar 
Yeh Y-C, Needham DM, Sieradzki ET, Fuhrman JA. Taxon disappearance from microbiome analysis reinforces the value of mock communities as a standard in every sequencing run. MSystems. 2018;3:e00023–18.Article 

Google Scholar 
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl Acids Res. 2013;41:D590–D6.CAS 
Article 

Google Scholar 
Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucl Acids Res. 2013;41:D579–D604.
Google Scholar 
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7.CAS 
Article 

Google Scholar 
Decelle J, Romac S, Stern RF, Bendif EM, Zingone A, Audic S, et al. Phyto REF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy. Mol Ecol Resour. 2015;15:1435–45.CAS 
Article 

Google Scholar 
Oksanen J, Blanchet F, Friendly M, Kindt R, Legendre P, McGlinn D, et al. Vegan: community ecology package. R package version 2.5-7. 2020. https://CRAN.R-project.org/package=vegan.Wickham H. ggplot2-elegant graphics for data analysis. Cham, Switzerland: Springer International Publishing; 2016.Kolde R. Pheatmap: pretty heatmaps. R Package Version. 2012;1:726.
Google Scholar 
Schloerke B, Crowley J, Cook D. Package ‘GGally’. Extension to ‘ggplot2’See. 2018;713. More