1. AGRRA : Introduction to Basic-level Coral Transects Revision: 2013-05-22 Judith Lang © K. Marks

2. The following images are Copyright © by New World Publications and by other photographers. Permission is granted to use the photographs and slides in this presentation with the AGRRA Program and, with attribution to the photographers and the AGRRA Program, for other valid educational purposes. All other uses are strictly prohibited. For permission to use their images, special thanks to: L. Benvenuti, A. Bruckner, J. Bruno, L. Chornesky, P. Dustan, R. Garza, J. Garzón, R. Ginsburg, R. Goodridge, P. Humann, B. Kakuk, M. Nugues, C. Rogers, R. Steneck, L. Williams, S. Zea

3. Basic-level Coral Transects Personnel minimum 2 trained divers Field Equipment (see AGRRA Equipment.pptx) clipboard or slate, with “Basic CORAL-UW-V5.5” datasheet printed on UW paper, & pencils Optional: “Coral CODES-V5.5” printed on UW paper 10-m long, lead-core rope, with marks at 1-m intervals, and tie-off loops at each end collapsible, 1-m pole marked in 10-cm units (see AGRRA Equipment.pptx) small, thin, plastic metric ruler 25 cm x 25 cm PVC quadrat around which to wrap the line. Optional: Dive thermometer or other temperature recording device

4. Unless instructed otherwise: avoid reef edges, unusual reef features, abrupt changes in slope, deep groves, large patches of sand or rubble, etc. MethodSurvey Overview -1 Before dive: fill in blank spaces at top of UW datasheet !!! At survey site: haphazardly set transect line on the reef. Avoid other benthic or coral transect lines. Pull taut; untangle if necessary, and secure. © after SCUBAnauts International no yes

5. Survey Overview -2 Record start time; bottom temperature (if you can); start depth (0 m) and end depth (10 m). Starting on one side of the line, sequentially survey all ≥ 4 cm stony corals, except for Millepora alcicornis, for which any part, no matter how small, is located inside a 50-cm-wide belt between the 0-m and the 10-m marks. transect line 50 cm include this include these © M. Ibrahim

6. Survey Overview -3 Then try to continue in a 50-cm-wide belt on the 2nd side of the transect line, being careful not to resurvey corals that are under the line. If survey cannot be completed during one dive (e.g., due to a large number of corals), tally by species all remaining ≥ 4 cm corals as colonies, clumps or fragments. © M. Ibrahim transect line 50 cm ignore this ignore these include this

7. Important! Pay close attention to any lionfishes (Pterois spp.) that remain in the immediate vicinity of the transect line during your survey! © K. Marks

8. Remember If the line sways a little due to strong surge or bottom current: note its position in the middle of its swing to locate the center of the belt. © M. Ibrahim

9. Examine every ≥ 4 cm coral, and note: Its Species code. The number of any Isolates, or its status as a Clump or Fragment. Its Size. Species, Isolates, Size © R. Garza

10. © K. Marks SSID = Siderastrea siderea SSID Species -1 Identify each scleractinian coral and Millepora (except M. alcicornis) by its CARICOMP-based code: 1st letter of genus + 1st 3 letters of species e.g., Pseudodiploria strigosa = PSTR Or, if unsure of the species, 1st 4 letters of the genus e.g., Orbicella annularis complex = ORBI EFAS = Eusmilia fastigiata © K. Marks EFAS

11. APAL APALPPOR © C. Rogers branching PAST SSID © R. Steneck mound OFAV If you don’t recognize a coral, sketch its shape and briefly describe. Try to identify it after the dive. Common Caribbean-area corals by shape and relative size. UAGA © M. Nugues © R. Steneck MCOM plate/keel EFAS flower MDEC nodules/crust © K. Marks Species -2

12. DCYL = Dendrogyra cylindrus Include all completely (standing) dead corals by the shapes of the colony or their corallites–if they can be identified at least to genus and are still mostly intact. Ignore dead branching corals in which most of the branches are missing because their original sizes cannot be estimated. Try to give the code or name for this standing dead coral: © R. Goodridge Species -3

13. Isolates -1 For each ≥ 4 cm colonial or solitary coral, note the number of soft tissue isolates caused by external perturbations. © E. Muller Put 0 if standing dead, i.e., the skeleton is intact but has no live tissues. 0 APAL

14. PSTR 1 2 3 © K. Marks 4 1 SCUB Isolate number, which reflects the effects of on-going or earlier disturbances, is likely to increase after partial-mortality events, like severe bleaching or an outbreak of disease. Put 1 if soft tissues are not sub-divided by any externally produced disruptions. If >10 isolates, round to the nearest 5, e.g.,15, 20… Isolates -2

15. Ignore the isolates that form naturally in some corals, and give these colonies a score of 1. ©A. Bruckner OANN 1 1 EFAS © K. Marks A colony is one genetic individual, even when its soft tissues naturally subdivide into separate units. Isolates -3

16. ©C. Rogers How many isolates are visible in this APAL? 1 234 5 7 6 © C. Rogers Isolates -4

17. How many isolates do you see in this coral? © K. Marks SINT 1: its soft tissues are continuous, despite the old mortality!1 Isolates -5

18. Locating a coral’s margins is necessary in order to count the number of isolates and measure its size. DLAB with arrows along its margin © J. Lang Colony margins can be difficult to locate when parts of a coral have died or broken away. DLAB Isolates -6

19. Colony margins can be difficult to locate when other colonies of the same, or similar species, occur close by, or even on, its skeleton. arrows show margin of OANN Live OFAV © J. Lang Dead OFAV OANN Isolates -7

20. Colony margins can be difficult to locate when parts of a coral are dead and being overgrown by other organisms. Whenever possible, look for connections between the live tissues or basal skeleton, and for similarities in the size and colour of the separated live tissues. Palythoa (a zoanthid) is overgrowing a PSTR. There are 2 isolates of one PSTR colony, not 2 colonies of PSTR. PSTR PAL © E. Chornesky 11 22 Isolates -8

21. Is this 1 colony of PSTR or 2? Examine the polyps in the separate areas: are they similar in color, shape and size? Examine the dead areas (from the side or base): does a common skeleton connect the polyps? © B. Kakuk LivePSTR LivePSTR DeadPSTR A closer look than is really possible with this image revealed a single base – these are 2 isolates of 1 coral! Isolates -9

22. Write CLUMP if you can’t distinguish colony borders. Clump A clump is a group of closely crowded corals of the same species for which individual colony margins cannot be distinguished by visual examination. PPOR © K. Marks © C. Rogers OANN Do not try to count # isolates for CLUMPS.

23. Do not count # isolates for FRAGS. Ignore hereafter. Fragment Write FRAG (=fragment) for each broken (or detached and easily moved) coral. © K. Marks Storm-generated fragments FRAG FRAG FRAG FRAG APRO FRAG

24. Find the direction in which the coral is growing. Look directly down at the coral at right angles to its growth direction = in planar view. Size -1 Measure the maximum* size of each colony, solitary coral or clump (but no fragments) that is at least 4 cm in length in planar view. * Maximum = include all its live and dead areas.

25. Record sizes to the nearest: 1 cm up to 10 cm, 5 cm up to 50 cm, 10 cm up to 200 cm, 20 cm up to 500 cm, 50 cm if > 5 m (i.e., in a large clump). Max Length : the longest distance across the outer surface of the coral. plan view = from above Max Width: the widest part of the coral perpendicular to its maximum length. Size -2

26. Max Height: parallel to the axis of growth, as seen from the side of the colony. Species of corals differ in how large they can grow and in the size at which they reach sexual maturity. Small corals are more likely to be completely killed by perturbations that cause partial mortality (i.e., kill some of their tissues). A reef without large corals may be recovering from a serious perturbation; one without recruits has no future. Size -3

27. Measure the maximum sizes of large colonies and clumps even when they extend outside the belt transect. Max L and Max W in a clump of APAL © C. Rogers Max L Max W APAL Size -4

28. © K. Marks Find Max Height in this DLAB. Max Height Remember to include the dead areas! Size -5

29. © J. Lang Look for Max Length, Max Width, and Max Height in this SSID. Max Width Max Length Max Height in this area Size -6

30. Find the approximate margins of this OFAV © J. Lang live dead dead dead dead dead Size -7

31. Now approximate its Max Length and Max Width © J. Lang Max. Width Max. Length Size -8

32. If fallen and, as yet, shows no reoriented growth: measure as if in original growth position. Include any coral that has fallen and is likely to survive, either because it is wedged in a crevice or because of its large size and/or weight. Locate the original Max Length and original Max Height for this recently fallen coral Max L Max H Size -9

33. Locate the original Max Length and the original Max Height in this large, heavy, fallen OFAV © SCUBAnauts International original Max L original Max H Size -10

34. If fallen and wedged or shows reoriented growth: measure in new growth position. © Ken Marks APAL reoriented reoriented reoriented Reoriented growth in a fallen APAL Size -11

35. Locate the new Max Length and the new Max Height for the fallen OFAV © SCUBAnauts International new Max H new Max L Size -12

36. Examine the entire surface of each colony, solitary coral or clump (but no fragments), and note any: Disease, code as X, or identify by disease code if so instructed by team leader. Bleaching, code as P (pale) and/or PB (partly bleached) and/or BL (all soft tissues are fully bleached) Mortality, code as NM (new mortality) and/or TM (transitional mortality) and/or OM (old mortality) or SD (standing dead) Condition

37. Codes for Common Diseases DS = Dark Spots © A. Bruckner SSID DS WP = White Plague © J. Miller WPWP OANN YB = Yellow Band © R. Ginsburg YB OFAV BB = Black Band © C. Rogers BB PSTR Condition -2

38. P = Pale PB = Partly Bleached (BL + P or unbleached) BL = Fully Bleached Coding should be based on local knowledge of the colours “normally” characteristic of each species at the given site. Codes for Bleaching BL = Bleached notbleached © L. Williams BL CNAT DLAB PB = Partly Bleached P BL SSID © K. Marks Condition -3

39. BL = Bleached SSID Some bleached corals glow pale purple, pink or blue! © R. Ginsburg BL SSID Condition -4

40. Codes for Mortality NM = New Mortality. White skeletons are intact (unless live tissues have just been bitten by a fish or abraded), with no visible sediment, algae, etc. Conspicuous during outbreaks of disease, bleaching- related mortality events, and just after hurricanes or other large-scale perturbations. Polyps would have died within the previous few seconds to several days. NM NM = New Mortality in MLAM Close-up alive © P. Dustan MLAM Condition -5

41. New polyps regenerating over scars initially are pale (= lack zooxanthellae); do not confuse with bleaching. © J. Lang regeneratingpolyps NM PAST NM = New Mortality in PAST Condition -6

42. When part of a coral dies, other organisms may quickly start to colonize the exposed skeleton. © K. Marks NM APAL NM = New Mortality live sparse turf algae dying polyps Condition -7

43. TM = Transitional Mortality © P. Dustan TM (turf algae) APAL(Close-up) new mortality TM = Transitional Mortality. Skeletons are mostly intact and covered with a thin layer of sediment or biofilms, or tiny, multi-colored turf algae (unless they have just been bitten by a fish or abraded). Polyps would have died within the previous days to months. Conspicuous soon after outbreaks of disease, bleaching- related mortality events, hurricanes or other perturbations. Condition -8

44. In addition to BB (black band disease), what can be seen in this severely stressed CNAT? © L. Benvenuti BB CNAT TMNMBL Condition -9

45. DSTRClose-up alive OM (turf algal sediment mat) OM = Old Mortality. Skeletons are covered with thick algal turfs, seaweeds or benthic animals that aren’t easily removed (unless these organisms have just been bitten by a fish or abraded). Polyps would have died within the previous months to years or decades to centuries. OM = Old Mortality Areas of OM can accumulate over very long periods in long-lived corals. © J. Lang (Close-up) PSTR OM live Condition -10

46. What kinds of mortality can be seen in this OFAV? © J. Lang live OM TMOMOM NM OFAV Condition -11

47. Post-Bleaching Mortality post-bleaching disease: same tissues have died severe bleaching: tissues survive Monitored OANN in St. John, U.S.V.I. © J. Miller Sept. 2005 BL © J. Miller Nov. 2005 TM Stony corals may initially survive severe bleaching but later die from a disease or other stressors. Repeat coral surveys may be required after severe bleaching events –e.g., in the NE to E Caribbean in 2005. Condition -12

48. MCAV = Montastraea cavernosa SD = Standing Dead. Entire coral has died but it can be identified to species, species complex, or genus. © K. Marks SD Give the species code for this SD coral. Condition -13

49. © K. Marks Optional Comments © R. Garza Note any obvious signs of predation or competition. Be sure to define any unique codes used here. Note if the coral is loose, wedged or reattached.

50. Codes for Common PredatorsHCAR feeding scar © P. Dustan HCAR = fireworm APAL © L. Benvenuti CABB = snail (algae on shell) foot © B. Kakuk DFG DFG = damselfish algal garden OANN PFB PFB = parrotfish bites © B. Kakuk OFAV Optional -2

51. LOB = Lobophora LOB © K. Marks HAM = Halimeda mat HAM © K. Marks DIC = Dictyota © K. Marks DIC Codes for Common Algal and Cyanobacterial CompetitorsCloseup TAS TAS = turf algal sediment mat PSTR © J. Lang CYAN = cyanobacteria © K. Marks CYAN Optional -3

52. CHON = Chondrilla caribensis Codes for Common Animal Competitors Or try to identify the AINV group, e.g., SPO = sponge TSOL = Trididemnum solidum © B. Kakuk TSOL UAGA ECAR = Close-up ORBI ECAR NM © A. Bruckner Erythropodium caribaeorum DLAB © K. Marks CDEL = Cliona delitrix CDEL © B. Kakuk CHONORBI Optional -4

53. Periodically check your bottom time and air supply. If remaining time and available air both permit, after completing the belt on one side of the line, return along the second side, assessing all ≥ 4 cm corals that are at least partially within a 0.5-m wide belt. Be careful not to resurvey any coral beneath the line that was examined during the first transect. Which 3 corals should be ignored as you return?. 1 2 3 50 cm transect line

54. If at any time during the dive you don’t have enough time and/or air left to complete the survey, use any blank spaces remaining on your datasheet to tally (= count and record) by name code and type all remaining corals: COL – SSID |||| |||| ||, CNAT |||| | CLUMP – PPOR | FRAG – PDIV ||| = 12 colonies of SSID & 6 of CNAT, 1 PPOR clump, 3 PDIV fragments Be careful not to confuse tallies and numbers: || = two, not eleven! Record the number of m 2 in which the corals were surveyed and the number of m 2, if any, in which the corals were tallied by their coral codes. Remember that the area between each 1-m mark on one side of the transect line = 0.5 m 2. This information is important for standardized coral density estimates.

55. In high-relief reefs with tall columnar corals, it may be easier to survey both sides of the line at the same time. You should still try to spread your assessment along the line in reefs containing too many corals to complete the entire 10 m 2 survey within one dive. Survey as group 1, 2, 3, 4… transect line 50 cm 1 2 3 4 ignore this

56. Transect and Site Comments Remember to define any unique codes used for coral condition and record numbers of any lionfishes. Record any important comments about the transect or site, e.g., if any other kind of benthic plant or animal is conspicuously damaged by bleaching, disease, or some other perturbation, note: its name or species code; its approximate abundance by % cover or number; the approximate % cover or number affected by the perturbation. Bleaching Palythoa (PAL) an excellent, early-bleaching indicator! © K. Marks BL “normal”

57. © J. Bruno Gorgonia (sea fan) Be sure to alert the appropriate authorities! Diseases Octocorals and sponges sometimes show conspicuous signs of disease (arrows). Name if you can, or sketch and briefly describe the appearance of the organism and its disease. Try to identify later. Xestospongia (barrel sponge) © B. Clark

58. Survey Review Starting on one side of the line, survey all ≥ 4 cm stony corals, except M. alcicornis, for which any part is located in a 50-cm wide belt between the 0-m and the 10-m marks. Then continue in a 50-cm-wide belt on the 2nd side of the transect line, being careful not to resurvey corals that are under the line. If too many corals to survey in one dive, tally by species all remaining ≥ 4 cm corals as colonies, clumps or fragments. Be sure to record any Site Comments by end of the dive. Data Entry Enter daily in a new data entry spreadsheet for each site and check to ensure accuracy of transcription. Back up your data files every day!