knowledge of the physical processes that contribute to variability in the coupled air-31 sea climate system within the Indonesian seas, which in turn also affects the marine 32 ecosystem at the heart of the ecologically important Coral Triangle. 33The tropical Indonesian seas play a central role in the climate system. They lie at 34 the climatological center of the atmospheric deep convection associated with the 35 ascending branch of the Walker Circulation. They also provide an oceanic pathway for 36 the Pacific and Indian inter-ocean exchange, known as the Indonesian Throughflow 37 (ITF), conveying the only link in the global thermohaline circulation at tropical latitudes 1 . 38As such, the volume of heat and freshwater carried by the ITF are known to impact the 39 state of the Pacific and Indian Oceans as well as the air-sea exchange 2-6 , modulating 40 climate variability on a variety of time scales. Sea surface temperature (SST) anomalies 41 3 over the Indonesian seas are associated with both the Pacific El Niño-Southern 42 Oscillation (ENSO) and the Indian Ocean Dipole (IOD), causing changes in the regional 43 surface winds that alter precipitation and ocean circulation patterns within the entire 44 Indo-Pacific region 7,8 . Indeed, proper representation of the coupled dynamics between the 45 SST and wind over the Indonesian seas is required for a more realistic simulation of 46The ITF had originally been thought of as occurring within the warm, near surface 48 layer with a strong annual signal driven by seasonally reversing monsoons 10 . However 49 recent observations reveal the inter-ocean exchange primarily occurs as a strong velocity 50 core at depth within the thermocline and exhibits large variability over a range of time 51 scales 11,12 . Ongoing in situ measurements indicate that the vertical profile of the flow has 52 changed significantly over the past decade. In particular there has been a prolonged 53 shoaling and strengthening of the ITF subsurface core within the Makassar Strait inflow 54 channel occurring in concert with the more regular and stronger swings of ENSO phases 55 since the mid-2000s 13 . On longer time scales, coupled models reveal that reduced Pacific 56 trade winds will correspondingly reduce the strength and change the profile of the ITF. 57These changes have important implications to the air-sea coupled system, since it is the 58 vertical profile of the ITF that is critical to the climatically relevant inter-basin heat 59 transport 12 . 60In this article we discuss recent observational evidence supported by models that 61show how recent changes in the wind and buoyancy forcing affect the vertical profile and 62properties of the flow through the Indonesian seas. Intense vertical mixing through 63 vigorous tides and strong air-sea interaction set the vertical stratification of the ITF 64 4 flow 14 , and is found to impact both ENSO and the IOD variability through thermocline 65 and wind coupling 9,15 . We highlight how these changes have direct consequences for the 66 ocean...
The Makassar Strait throughflow of ~12–13 Sv, representing ~77% of the total Indonesian Throughflow, displays fluctuations over a broad range of time scales, from intraseasonal to seasonal (monsoonal) and interannual scales. We now have 13.3 years of Makassar throughflow observations: November 1996 to early July 1998; January 2004 to August 2011; and August 2013 to August 2017. Strong southward transport is evident during boreal summer, modulated by an ENSO interannual signal, with weaker southward flow and a deeper subsurface velocity maximum during El Niño; stronger southward flow with a shallower velocity maximum during La Niña. Accordingly, the southward heat flux, a product of the along‐channel current and temperature profiles, is significantly larger in summer and slightly larger during La Niña. The southward flow relaxed in 2014 and more so in 2015/2016, similar though not as extreme as during the strong El Niño event of 1997. In 2017, the throughflow increased to ~20 Sv. Since 2016, the deep layer, 300‐ to 760‐m southward transport increases, almost doubling to ~7.5 Sv. From mid‐2016 into early 2017, the transports above 300 m and below 300 m are about equal, whereas previously, the ratio was about 2.7:1. Near zero or northward flow occurs in the upper 100 m during boreal winter, albeit with interannual variability. Particularly strong winter reversals were observed in 2014/2015 and 2016/2017, the latter being the strongest winter reversal revealed in the entire Makassar time series.
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