Seaweed

All of the marine and terrestrial samples were collected in 2001–2013 from a stony shore and a farm in Yugawara (35°08′N, 139°07′E), Japan, respectively. The stony shoreline surveyed represented ∼0.2 hectares and ranged in depth from 0 to 5 m, where brown and red macroalgae are dominant primary producers but seagrass is absent. The farm was also approximately 0.2 hectares with cultivation of fruits and vegetables, all of which were C₃ plants. Green leaves and/or nuts were collected for higher plants, and whole samples of 1–15 individuals within a single stage were collected for the other species. The collected samples were cleaned with distilled water to remove surface contaminants and stored at −20°C. For most terrestrial species and marine macroalgae, whole-organism samples were prepared for isotopic analyses. For the remaining marine specimens, small samples of muscle tissue were taken. Shell samples were taken from several gastropod and lobster specimens, and scales were dissected from most of the fish species (Appendices A1 and A2). There was no substantial effect on the trophic position estimates among these different tissue types within a single animal specimen (e.g., Chikaraishi et al. 2010 , 2011 ; Ogawa et al. 2013 ). The bulk-carbon and bulk-nitrogen isotopic compositions of representative samples (40 coastal marine and 69 terrestrial samples, Appendices A1 and A2) were determined using a Flash EA (EA1112) instrument coupled to a Delta^plusXP IRMS instrument with a ConFlo III interface (Thermo Fisher Scientific, Bremen, Germany). Carbon and nitrogen isotopic compositions are reported in the standard delta (δ) notation relative to the Vienna Peedee Belemnite (VPDB) and to atmospheric nitrogen (AIR), respectively.
The nitrogen isotopic composition of amino acids was determined by gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS) after HCl hydrolysis and N-pivaloyl/isopropyl (Pv/iPr) derivatization, according to the procedure in Chikaraishi et al. (2009 ) (which are described in greater detail at http://www.jamstec.go.jp/biogeos/j/elhrp/biogeochem/download_e.html). In brief, samples were hydrolyzed using 12 Mol/L HCl at 110°C. The hydrolysate was washed with n-hexane/dichloromethane (3/2, v/v) to remove hydrophobic constituents. Then, derivatizations were performed sequentially with thionyl chloride/2-propanol (1/4) and pivaloyl chloride/dichloromethane (1/4). The Pv/iPr derivatives of amino acids were extracted with n-hexane/dichloromethane (3/2, v/v). The nitrogen isotopic composition of amino acids was determined by GC/C/IRMS using a 6890N GC (Agilent Technologies, Palo Alto, CA) instrument coupled to a Delta^plusXP IRMS instrument via a GC-C/TC III interface (Thermo Fisher Scientific, Bremen, Germany). To assess the reproducibility of the isotope measurement and obtain the amino acid isotopic composition, reference mixtures of nine amino acids (alanine, glycine, leucine, norleucine, aspartic acid, methionine, glutamic acid, phenylalanine, and hydroxyproline) with known δ¹⁵N values (ranging from −25.9‰ to +45.6‰, Indiana University, SI science co.) were analyzed after every four to six samples runs, and three pulses of reference N₂ gas were discharged into the IRMS instrument at the beginning and end of each chromatography run for both reference mixtures and samples. The isotopic composition of amino acids in samples was expressed relative to atmospheric nitrogen (AIR) on scales normalized to known δ¹⁵N values of the reference amino acids. The accuracy and precision for the reference mixtures were always 0.0‰ (mean of Δ) and 0.4–0.7‰ (mean of 1σ) for sample sizes of ≥1.0 nmol N, respectively.
The δ¹⁵N values were determined for the following 10 amino acids: alanine, glycine, valine, leucine, isoleucine, proline, serine, methionine, glutamic acid, and phenylalanine (Appendices A1 and A2). These amino acids were chosen because their peaks were always well separated with baseline resolution in the chromatogram (Chikaraishi et al. 2009 ). Also, it should be noted that glutamine was quantitatively converted to glutamic acid during acid hydrolysis; as a result, the α-amino group of glutamine contributed to the δ¹⁵N value calculated for glutamic acid.
The TP_Glu/Phe value (and its potential uncertainty calculated by taking into account the propagation of uncertainty on each factor in the Eq. (1)) was calculated from the observed δ¹⁵N values (as 1σ = 0.5‰) of glutamic acid and phenylalanine in the organisms of interest, using eq. (1) with the β value of −3.4 ± 0.9‰ for coastal marine and +8.4 ± 1.6‰ for terrestrial samples, and with the TDF value of 7.6 ± 1.2‰ for both ecosystems, according to Chikaraishi et al. (2009 , 2010 , 2011 ). The TP_Tr/Scr values were not calculated, because we did not measure the δ¹⁵N values of lysine and tyrosine for all investigated samples and of serine for approximately a half of samples.

The self-administered FFQ includes question items on the average frequency of consumption during the past year with the following eight possible responses: almost never, 1–3 times per month, 1–2 times per week, 3–4 times per week, 5–6 times per week, once per day, twice per day, and ≥ 3 times per day. These responses are then converted into intake scores of 0, 0.1, 0.2, 0.5, 0.8, 1, 2, and 3, respectively, to approximate the intake frequency per day. The consumption of foods is tabulated in grams for 20 food groups based on the Standard Tables of Food Composition in Japan (seventh revised edition) [14 ]. The food groups (shown as the number of items: description) were rice (1), bread (1), noodles (1), potatoes (1), soybean products (4: tofu in miso soup, tofu dishes, fermented soybeans [nattō], and fried tofu [ganmodoki]), green vegetables (5: pumpkin, carrot, broccoli, green-leaf vegetables, and other green-yellow vegetables), other vegetables (5: cabbage, radish, dried radish [kiriboshi-daikon], bamboo shoots, and other vegetables), fruit (2: citrus fruits and other fruits), mushrooms (1), seaweeds (1), fish (7: fish, bone-edible small fish, canned tuna, octopus/shrimp/crab, shellfish, fish eggs, and fish paste products), meat (4: chicken, beef/pork, liver, and ham/sausage/bacon), eggs (1), milk (2: milk and yogurt), oils (6: margarine, butter, mayonnaise, deep-fried dishes, light-fried dishes/sauté, and peanuts/almonds), confectionery (2: Western- and Japanese-style confectioneries), green tea (1), coffee (1), alcoholic beverages (1), and soybean paste (1).
The FFQ contains no question items on usual portion size for 43 food items, so we applied the standard portion sizes based on DRs in a population from Aichi Prefecture [3 (link)]. However, portion sizes are requested for three kinds of staple foods in Japan (rice, bread, and noodles). The daily consumption of each food item was computed by multiplying the portion size by the intake score. For alcoholic beverages, the amount and frequency per week or month were asked for the following 10 items: sake, Japanese liquor (shōchū), shōchū highball, large bottle of beer (633 mL), medium-sized bottle of beer (500 mL), 350 mL of canned beer, 250 mL of canned beer, single whiskey, double whiskey, and wine. Sugar-sweetened beverages (SSBs) were not included in the short FFQ.

A field survey to assess whether patterns of bleaching of Pocillopora differed between colonies within a farmerfish garden (territory) and those on adjacent, unprotected substrate was conducted during June and July 2019 before bleached tissues of coral died or recovered. Divers assessed all Pocillopora colonies found on 178 haphazardly encountered bommies that were scattered throughout the 2 x 0.5 km study polygon. The bommies varied in the amount of their surface covered by Stegastes gardens, from lacking gardens altogether to those that were partially to completely covered. Gardens were readily identified by their lush growth of turf red algae (commonly Polysiphonia spp.) and the presence of Stegastes; the substrate surface not defended by farmerfish typically had closely cropped turf and/or crustose coralline algae. All surveyed bommies were measured (L x W x H) and the location of Pocillopora colonies noted (outside or inside of a garden if present). Colonies were then placed into 1 of 5 diameter categories (< 3 cm, 3–10 cm, 11–20 cm, 21–30 cm, > 30 cm dia; see [11 (link)]). Each Pocillopora was photographed, and the proportion of the colony that was (1) alive and unbleached, (2) alive but bleached (i.e., tissues transparent and underlying skeleton visibly white), and (3) dead (no tissue and skeleton overgrown with algae from previous partial mortality) was estimated visually in the field (the 3 categories sum to 1). The live but bleached category was defined as tissue that had substantially lower or no pigmentation (due to lower levels of Symbiodiniaceae) relative to the rest of the colony and followed the Australian Coral Watch Coral Health Chart for scoring coral bleaching (https://coralwatch.org). Quantification of bleaching was made by the same individual (RNH). If present on a bommie, Stegastes garden sizes were measured, and the number of adult farmerfish enumerated. A total of 1,137 Pocillopora colonies was assessed on the 178 bommies surveyed.
Due to the need for a rapid assessment of bleached corals, the total amount of the two ‘substrate types’ (inside vs outside farmerfish territories) in the study area was not estimated during the June to July 2019 survey. Not all the non-garden area of a bommie was suitable for occupancy by Pocillopora since varying portions of the Porites coral bommies were still alive and/or occupied by other benthic space holders such as macroalgae. We used a recent survey of benthic habitats of the study site to estimate the relative areas of garden vs non-garden habitats that were suitable for occupation by Pocillopora as an approximation of the relative sampling effort for the two habitat types. The 2016 benthic survey consisted of 24 band transects each 20 x 5 m where the substrate / space holder was identified at every 0.5 m point on the grid (i.e., 492 point samples per band transect). The benthic categories quantified included, among others, Stegastes gardens, other turf algae, crustose coralline algae (CCA), live coral (by genus or species), live portions of Porites bommies, and macroalgae (by genus or species). The 24 transects were distributed more or less evenly from the mid-lagoon to fringing reef along the 2 km span of the study site. These data were used to estimate the mean proportion of hard substrate at the study site that was covered by farmerfish gardens, and the mean proportion of non-garden hard substrate that was or could have been occupied by branching corals (i.e., cover of branching coral + cover of cropped turf algae / CCA on bommies).
In addition to exploring how Pocillopora responded to the bleaching event as a function of position within or outside a farmerfish territory, responses as a function of colony size also were explored as other studies in Moorea have shown that for a variety of reasons, larger and smaller colonies of Pocillopora can have different susceptibilities to bleaching [4 (link), 30 (link)]. Accordingly, the 1,137 surveyed corals were divided into two size classes, small (≤ 10 cm dia) and large (> 10 cm dia). Several statistical tests were conducted to explore relationships between Pocillopora colony size and location (inside or outside of a garden) with two metrics of bleaching (prevalence and severity, see below). All analyses were performed using the R language for statistical computing version 4.1.1 [38 ].