relatively extensive shallow water and true continental shelf are a platform west of the Vogelkop Peninsula and to the south where Papua shares a common continental shelf with northern Australia. Surface currents are somewhat mixed in this region, however a northward current flows between Papua and Halmahera and an eastward current flows along the north shore of Papua during the northeast monsoon. This pattern reverses during the southeast monsoon.
The Raja Ampat Archipelago includes the four large islands of Waigeo, Batanta, Salawati, and Misool and hundreds of smaller islands. Ecological Rapid Assessments through the Raja Ampat Islands in 2001 and 2002 visited a total of 45 and 59 sites, respectively, surveying coral, mangrove, seagrass, other marine habitats, and turtle nesting beaches (McKenna, Allen, and Suryadi 2002; Donnelly, Neville, and Mous 2003). Substantial shallow seagrass meadows of T. hemprichii, C. rotun-data, and H. uninervis were reported on Sayang Island, in the bays on the southeastern side of Kawe, on reefs off the northern Waigeo coast and at Deer Island off the northern coast of Kofiau (Donnelly, Neville, and Mous 2003; Hitipeuw 2003). In the south of the archipelago, extensive seagrass meadows of E. acoroides and S. isoetifolium have been reported on the reef flat of Batanta Island (Tomascik et al. 1997; Scheltze-Westrum 2001). Seagrasses were also recorded at Kri Island, Pef Island, Waigeo Island (Mayalibit Passage), Wruwarez Island, the northwest side of Batanta Island, North Fam Island, Batang Pele Island, Wofah Island and Yeben Kecil Island (McKenna, Allen, and Suryadi 2002).
The seagrasses reported from northern coast of the Vogelkop, east of Sorong District, include S. isoetifolium, C. serrulata, C. rotundata, H. pinifolia, H. spinulosa, H. ovalis, T. hemprichii, and E. acoroides (Tomascik et al. 1997, Kuriandewa et al. 2003; see Table 5.3.3). There is however, little or no information describing the reef communities further east around Vogelkop Peninsula.
An ecological Rapid Assessment of Biak and the Supiori Islands in 1996 found nine seagrass species (T. hemprichii, C. rotundata, C. serrulata, H. uninervis, H. pinifolia, E. acoroides, H. ovalis, H. minor, and S. isetofolium; MREP 1996), of which C. rotundata and T. hemprichii were the most widely distributed, creating high density monospecific meadows (1,276 shoots per m2; Kuriandewa et al. 2003).
A prominent feature of the reefs in the Padaido Islands (south of Biak Island) is the presence of extensive reef-top seagrass meadows (530 ha) dominated by Cymodocea spp., E. acoroides, and T. hemprichii (Tomascik et al. 1997). The western extremity of the Padaido Islands has a dense coverage (95–100%) of seagrass over 529 ha of shallow reef flat, consisting of seven species (T. hemprichii, C. rotundata, C. serrulata, H. uninervis, H. pinifolia, E. acoroides, and H. ovalis). Similarly, extensive reef top seagrass meadows (T. hemprichii, C. rotundata, H. ovalis, and H. pinifolia) have been reported on Numfoor Island (Tomascik et al. 1997) and along the southern coast of Yapen Island.
Cenderawasih Bay National Park (established in 1994) is the largest marine park in Southeast Asia and the only marine park in the region. Extensive lagoonal seagrass meadows (T. hemprichii, C. rotundata, H. uninervis, E. acoroides, and H. ovalis) are present along the mainland coast of southwestern Cenderawasih Bay, particularly in Wandammen Bay (Nietschmann et al. 2000). The vast seagrass meadows in this bay are reported to harbor a large dugong population (Petocz, 1989). Maruanaya (2000) reported three species of seagrass in the same region covering an area of 24 ha on the seaward side of mangrove areas with average density of 56 shoots per m2. Fringing reefs surrounding the many small islands in the region are also covered with seagrass meadows, including Pepaya Island (near Nabire) (Chou et al. 2002).
Virtually nothing is known of marine ecosystems along the north coast of Papua. The north coast is almost reef free and continues as such from Cenderawasih Bay to Sarmi, with only very occasional areas of fringing reef about some of the small islands (Spalding, Raviolus, and Green 2001). Further east, fringing reefs are believed to follow a large proportion of the coastline to the border with Papua New Guinea. For the most part these are poorly described, but reef flats are estimated to reach 300–400 meters wide in places. Tomascik et al. (1997) reported six seagrass species (C. rotundata, E. acoroides, H. ovalis, C. serrulata, T. ciliatum, and T. hemprichii) on the near continuous fringing reefs from Jayapura to the border with PNG.
Relatively little is known about the seagrasses along the shores of southern Papua. This area of the coastline has extensive mangrove forests. Over half the area of mangroves in Indonesia are located in Papua (Spalding, Blasco, and Field 1997). Bintuni Bay, which contains more than 1.1 million acres of mangroves, is the world’s third largest mangrove area and the second largest in Asia.
However, the only seagrass known in the bay is an anecdotal report from Berau Bay (the west side of Bintuni Bay) (Jamartin H. S. Sihite, pers. comm.). No sea-grasses were located anywhere else within Bintuni Bay or within the open, deeper waters (up to 60 m) towards McCluer Gulf (Erftemeijer, Allen, and Zuwendra 1996). This is possibly a consequence of the high turbidity throughout Bintuni Bay: secchi depths (a parameter used to measure the clarity of surface waters) of 11 to 85 cm in the mangrove area (creeks and rivers) and maximum 157 cm in the open waters of the bay (Erftemeijer, Allen, and Zuwendra 1996). Unfortunately Bintuni Bay marine ecosystems are increasingly threatened by overharvesting, logging, and clearing to make way for coastal shrimp farm facilities. Although the Bintuni Bay Nature Reserve affords some protection, there are no seagrasses in the Reserve and economic development is increasing due to a new liquified natural gas field in the bay, and the human population is expanding rapidly.
Although there are other significant areas of mangroves and wetland areas with sago palms in the gulf near Timika, Mimika district, around the Asmat region, and surrounding Yos Sudarso Island, Merauke (Spalding, Blasco, and Field 1997), the presence of seagrass communities is unknown. Large amounts of sediment are found along the southeastern coast (apparent in remote images; see http://eosweb.larc.nasa.gov/; http://eol.jsc.nasa.gov/), which possibly prohibit reef development in this region. Significant land clearing, logging, and mine tailings may exacerbate sedimentation, further prohibiting seagrass growth in localized areas. For example, large tracts of mangrove were also cleared at the mouth of the Timika River to construct the Amamapare seaport and mine tailings are now polluting nearby coral reefs. As part of the Freeport-McMoRan Copper & Gold Inc. mine Long-Term Environmental Monitoring Program, monitoring of benthos occurs at 14 sites in the estuaries (e.g., Minajerwi River) and 40 sites in the Arafura Sea (http://www.fcx.com/envir/wtsd/2004/env-perform.htm). The monitoring indicates no impact of tailings on the marine benthos in the Arafura Sea outside of the tailings management area.
It is likely however, that seagrasses are present throughout this region as significant seagrass meadows surround the nearby Aru Islands, a group of about 95 low-lying islands (8,563 km2) in the Arafura Sea (Moluccas), southwest of Papua. These meadows are predominately E. acoroides, T. hemprichii, C. rotundata, and S. isoetifolium. H. decipiens has also been reported from the deeper waters in the north of the islands (Nietschmann et al. 2000) and possibly extends northward to the Papuan mainland coast. Expansive seagrass meadows, which support significant Green Sea Turtle populations, also surround the adjacent Kai Islands, Kai Kecil and Kai Besar (Suárez 2001).
South of this region are the expansive seagrass meadows of the Torres Strait. The Torres Strait is a shallow (mostly 10–20 m depth) body of water formed by a drowned land ridge extending from Cape York to southwestern Papua New Guinea. Seagrass communities occur across the open sea floor, on reef flats and subtidally adjacent to continental islands. The large expanses of open water bottom are covered with either sparsely distributed Halophila or mixed species (Halodule, Thalassia, and Syringodium) communities (Coles, McKenzie, and Campbell 2003). It is likely that these meadows may extend northward to the Merauke coast, but surveys (e.g., Long et al. 1995) have not included this region.
Johnstone (1982) considered that seagrass zonation,
