Sessile Benthic Marine Invertebrate Biodiversity at Ningaloo Reef, Muiron Islands, and Exmouth Gulf, Western Australia: A Review and Gap Analysis

Abstract

This paper provides a comprehensive review of sessile benthic invertebrate biodiversity across three interconnected marine areas in Western Australia’s Gascoyne and southern Pilbara regions: Ningaloo Reef (a UNESCO World Heritage site), the nearby Muiron Islands to its north, and Exmouth Gulf to its east. The study aims to identify taxonomic and spatial knowledge gaps and establish a baseline biodiversity record for the broader region. We collated specimen-based records from seven Australian museums and supplemented them with data from the Atlas of Living Australia, iNaturalist, and a Web of Science literature review. In total, we report 827 verified species of sessile benthic invertebrates in shallow waters (less than 30 m depth) across the Gascoyne and southern Pilbara regions from 4578 records. Ningaloo Reef exhibits the highest diversity, hosting 587 species, including 239 scleractinian corals and 124 sponges. Exmouth Gulf is home to a diverse and unique assemblage of at least 295 species, including 165 species of putative turbid water specialists or regionally restricted species which are not found at Ningaloo Reef or the Muiron Islands. Notably, all three sea pen species identified in this review are recorded exclusively from Exmouth Gulf. The Gulf also hosts a distinctive community of filter-feeding invertebrates, including 125 sponges, 27 tunicates, and 18 anemones that are not found in neighboring regions. The Muiron Islands, although under sampled, host 22 species of sponges, 14 octocorals, and 5 tunicates that have not so far been found at Ningaloo Reef or Exmouth Gulf, highlighting the uniqueness of the islands’ marine invertebrate fauna. The southern sector of Ningaloo Reef is under sampled, and there are gaps in the state faunal collections for many groups, including anemones, corallimorphs, zoanthids, cerianthids, and hydrozoans. Further targeted taxonomic research on existing museum collections is crucial, as only 18% of specimen records have been verified, and 41% of the verified records are only identified to morphospecies. This limits our understanding of regional diversity and distribution patterns but provides ample opportunity for further taxonomic study. Expanding monitoring programs to include Exmouth Gulf and the Muiron Islands, along with unique habitats such as the King Reef artificial reef, and conducting additional biodiversity, demographic, and ecosystem health research is essential to assess the cumulative impacts of climate change and other environmental stressors on the unique and culturally significant marine ecosystems of this region.

1. Introduction

The Ningaloo (Nyinggulu) Coast in the Gascoyne region of Western Australia is renowned for its rich marine biodiversity and unique hot, arid ecosystems [1]. For up to 60,000 years, this region, including Ningaloo Reef, the Muiron Islands, and Exmouth Gulf (Figure 1), has held cultural significance for the Baiyungu, Thalanyji, and Yinigurdira peoples [2]. Marine invertebrate communities in these three distinct ecosystems have been shaped by stark contrasts in environmental conditions (e.g., high turbidity in Exmouth Gulf), oceanographic factors (e.g., strong wave exposure at the Ningaloo Reef front), and human impacts (e.g., trawling in Exmouth Gulf).

Figure 1. Project Area Map. The project area was delineated into four subregions with the 30 m depth contour demarking the westerly limit.

Ningaloo Reef, a UNESCO World Heritage site, extends approximately 300 km along the Cape Range Peninsula and is one of the world’s largest western-facing fringing coral reefs. Protected since 1987 within the Ningaloo Marine Park (Figure 1), which covers about 5000 km², the park includes 18 sanctuary zones spanning ~1300 km², roughly 26% of its area. It is a hotspot for tourism; it experiences relatively low pollution levels and has Ecosystem-Based Fisheries Management Strategies for recreational and commercial fishing activities [3]. The reef is celebrated for its low-turbidity waters, resulting from minimal river runoff and an extensive scleractinian coral community. Summer winds generate the Ningaloo Current, which flows along the inner shelf and enhances nutrient availability in the lagoon, and the regional nutrient supply is enhanced through episodic upwellings [4,5]. The main reef consists of elongated segments separated by gaps that promote lagoon flushing, with an average depth of about 2 m [6]. In northern Ningaloo, a narrow continental shelf (sometimes less than 10 km wide) brings nutrient-rich waters close to the reef, boosting pelagic productivity and attracting migratory filter feeders like manta rays and whale sharks [7,8] along with a large sea turtle population that principally resides in the lagoonal areas [9,10].

Located about 15 km from Ningaloo Reef, the Muiron Islands are protected under the Muiron Islands Marine Management Area, which includes three conservation zones. The islands are remnants of ancient limestone formations with well-developed fringing coral reefs. Like Ningaloo, their waters are typically clear, influenced by the Leeuwin and Ningaloo Currents. Although ecologically connected to the broader Ningaloo region, the Muiron Islands are renowned for supporting a higher abundance of soft corals [11]. The greater prevalence of soft corals may be related to higher turbidity or nutrient levels due to the proximity to Exmouth Gulf, and the islands’ geographic position, which provides partial shelter from the dominant south-westerly swell that impacts Ningaloo Reef [1,12]. These factors are taken together to create favorable conditions for soft coral growth.

In contrast, Exmouth Gulf, just east of Ningaloo Reef, is a large (~3000 km²), shallow (5–22 m depth) subtropical estuarine embayment with turbid waters. It is influenced by the southerly flowing Leeuwin Current and experiences strong semi-diurnal tides, frequent cyclones, and riverine runoff from the Ashburton River, which contributes to persistent turbidity [4,13]. The Gulf’s reefs began developing at least 7500 years ago during the Holocene high stand [14], and several islands, including Eva I, Fly I, and Tent I, feature fringing reef platforms dominated by coralline algae, with hard coral cover ranging from 1% to 37% [15]. Additionally, there are at least 20 submerged reefs and shoals dominated by filter-feeding organisms like soft corals and sponges. The Gulf is not currently protected within any state or federal jurisdiction, and destructive activities like commercial prawn trawling, initiated in 1963 [16], contribute to persistent turbidity levels. The cumulative pressures and values of the Gulf are summarized in [17].

While extensive literature examines the diversity and movement patterns of megafauna such as whale sharks, manta rays, and various cetaceans and turtles in the region [7,9,10,18,19,20,21,22], fewer scientific publications focus on the diversity and conservation status of sessile invertebrates that are vital for habitat provision and the food chain. Over the past five decades, however, numerous scientific expeditions have been conducted, and much data are accessible through museums, reports, and online repositories like the Atlas of Living Australia.

The earliest collections of habitat-forming sessile marine invertebrates from Ningaloo Reef were conducted by the Western Australian Museum (WAM) in 1968, with subsequent collections in 1977, 1980, and 1981, focusing on scleractinian corals and culminating in Veron and Marsh’s 1988 book, Hermatypic Corals of Western Australia [23]. In 2008, the Australian Institute of Marine Science (AIMS) and WAM surveyed the area using the vessel RV Solander, followed by a 2009 partnership with Murdoch University to survey the Tantabiddi and Gnarloo regions. That same year, a consortium of museums and AIMS participated in the CReefs Census of Marine Life Project at Ningaloo Reef [24]. Additionally, WAM, AIMS, and others conducted surveys in 2002 and 2006 via the RV Cape Ferguson for the Ningaloo Deeper Water Biodiversity Project supported by the Western Australian Marine Science Institute (WAMSI) [25].

Turning to Exmouth Gulf, WAM surveyed the RV Naturaliste in 2004, followed by the Pilbara Marine Conservation Partnership: Seabed Biodiversity Characterization and Mapping project in 2013, which involved the Commonwealth Scientific and Industrial Research Organization (CSIRO) and partner organizations [26]. The Gulf was surveyed again in 2019 as part of a Bush Blitz Project [27]. In contrast, the Muiron Islands were only surveyed in 2016 as part of the Net Conservation Benefits project, highlighting a disparity in effort to assess the region’s marine biodiversity.

In this study we focus on filter-feeding and habitat-forming marine invertebrates, such as sponges and corals, because they play a critical role in shaping benthic ecosystems by creating complex habitats that support diverse communities. Their filter-feeding activity also improves water quality and drives nutrient cycling, sustaining ecosystem productivity and overall health. Understanding the diversity and distribution of these organisms is therefore essential for assessing ecosystem resilience and function [28].

This study provides a comprehensive review of sessile, filter-feeding, and habitat-forming benthic invertebrate diversity at Ningaloo Reef, the Muiron Islands, and Exmouth Gulf. Focusing on the phyla Porifera, Cnidaria, Bryozoa, and Chordata, we synthesize both specimen-based and verified photographic records to deliver an updated estimate of biodiversity within these taxa across the region.

More specifically, we aim to achieve the following:

(1)

summarize the existing sessile benthic biodiversity records in this region.

(2)

pinpoint regions or taxon groups where knowledge is lacking.

(3)

recommend priority areas for biodiversity research to fill these gaps and improve understanding of the diversity and ecology of marine life in the region.

2. Methods

To obtain specimen-based records of sessile benthic organisms from the phyla Porifera, Cnidaria, Bryozoa, and Chordata, we contacted seven Australian museums: the Western Australian Museum (WAM), Australian Museum (AM), Museum of Tropical Queensland (MTQ), Queensland Museum (QM), South Australian Museum (SAM), Museum Victoria (MV), and the Museum and Art Gallery of the Northern Territory (MAGNT) to obtain a copy of all database records pertaining to our project area.

The project area lies at the boundary between the northern Pilbara and northern Gascoyne regions of Western Australia (Figure 1). The requested data focused exclusively on shallow water specimens (<30 m depth) from Ningaloo Reef Marine Park, the Muiron Islands Marine Management Area, and Exmouth Gulf, spanning a latitudinal range from 21°34′25.7″ S to 24°02′0.7″ S. The project area extends from the coastline in the east to the 30-m depth contour in the west. The study is confined to the 30 m depth contour due to the geomorphological constraints of Exmouth Gulf, which lacks habitats beyond this depth. This depth boundary was assigned to focus efforts on ecologically significant shallow reef communities in the photic zone. The 30-m depth contour was digitized from the AUS 746 and AUS 745 maritime charts, produced at a scale of 1:150,000 based on soundings, with AUS 746 last updated in 2010 and AUS 745 in 2012. We recognize potential inaccuracies in both the original charts and the digitization process. Ningaloo Reef was divided into northern and southern subregions with the boundary at Point Cloates. The Muiron Islands subregion was based on Marine Park boundaries, and the northern boundary of Exmouth Gulf extended from Harding River in the East to Vlamingh Point in the West (Figure 1).

Specimen-based Museum records were complemented by published data from the Atlas of Living Australia [29] and iNaturalist platforms [30]. Area searches on iNaturalist were conducted for the four regions mentioned above and are visualized in Figure 1. Additionally, a literature review using Web of Science was performed to identify relevant species-level records. The primary search terms included “Ningaloo,” “Exmouth Gulf,” and “Western Australia,” while secondary terms encompassed “biodiversity,” “taxonomy,” “benthic,” “porifera,” “bryozoan,” “cnidaria,” “tunicate,” “sponge,” and “coral.”

Specimen-based records for the four regions were complemented by published data from the Atlas of Living Australia (ALA), accessed on 2–30 August 2024 [29]. Records obtained from ALA included human observations from the online platform iNaturalist [30], and several other sources, including records from the West Australian Department of Biodiversity and Conservation (DBCA) [31], the Pilbara Marine Conservation Partnership (PMCP) [26], and the West Australian Marine Science Institute (WAMSI) [25]. In addition, ALA provides records from Museum database uploads, which were cross-checked with those provided directly by Museums. When necessary, duplicates were removed.

Specimen-based and digital search results were combined into a Microsoft Excel spreadsheet (Supplementary Table S1) for publication as Electronic Supplementary Material (ESM), including location information, data source, and registration numbers where available. Records obtained from iNaturalist (via ALA) include information on data quality (i.e., “research grade” or “human observation”). Higher-level taxonomic classifications were updated where necessary according to the World Register of Marine Species as of October 2024 [32].

Due to the significant number of specimens identified only at higher taxonomic levels (Phylum, Class, Order, Family, or Genus), it was essential to categorize records as either “verified” or “unverified.” All species-level (accepted Linnean species) records were classified as “verified”. However, we also classified morphospecies as “verified” (e.g., Sarcotragus sp. NW1). The utilization of morphospecies classification is widely employed in biodiversity assessments where species-level identification is infeasible [33,34]. Morphospecies delineations were treated as verified records because these specimens had been assessed by taxonomic experts, who confirmed that they were morphologically distinct from described species. For the remainder of this study, “morphospecies” will be referred to as “species”. In contrast, higher-level records (Genus, Family, or higher) were marked as “unverified” unless they represented the only known record for that taxon at the lowest practicable level. This approach allowed us to verify the presence of at least one species from that taxon, with the remaining records being treated as unverified.

Taxa were grouped into categories spanning Phylum (e.g., Porifera, Bryozoa), Subphylum (Tunicata), Class (Octocorallia, Zoantharia, Hydrozoa), and Order (e.g., Scleractinia, Actinaria, Antipatharia, Ceriantharia, Corallimorpharia) to allow analyses at ecologically meaningful scales that capture functional similarities while retaining sufficient taxonomic resolution.

3. Results

A total of 4578 specimen records were gleaned from museum databases and other faunal databases (Supplementary Table S1), and a total of 827 sessile benthic invertebrate species could be verified to occur in waters shallower than 30 m in the four regions examined in this study (Table 1). Five hundred eighty-seven species were collected or observed from Ningaloo Reef (185 from the southern sector and 510 from the northern sector), 86 from the Muiron Islands, and 295 from Exmouth Gulf.

Table 1. Total number of verified species/morphospecies per subregion and region within each taxonomic group.

	Region				Regional Totals
	Ningaloo South	Ningaloo North	Exmouth Gulf	Muiron Islands	Ningaloo Reef	Study Area
Phylum Bryozoa	5	69	9	0	71	78
Phylum Porifera	45	92	125	40	124	249
Subphylum Tunicata	3	9	27	11	12	37
Class Hydrozoa	2	7	6	1	9	15
Class Octocorallia (incl. Sea Pens)	56	82	47	20	108	159
Class Zoantharia	7	8	5	0	11	12
Order Actinaria	1	9	18	1	10	23
Order Antipatharia	1	0	2	0	1	3
Order Ceriantharia	0	1	1	0	1	2
Order Corallimorpharia	0	1	1	1	1	2
Order Scleractinia	65	232	54	12	239	247
Total	185	510	295	86	587	827

3.1. Porifera

A total of 249 verified species of Porifera were recorded in the project area. One hundred and twenty-four of these are recorded at Ningaloo Reef (Table 1), with 45 from the southern sector and 92 from the northern sector. One hundred and twenty-five species/morphospecies were also recorded from Exmouth Gulf and 40 from Muiron Islands, where they accounted for the greatest proportion of species diversity (Table 1, Figure 2). Fifty-eight percent of the sponges (n = 473) were identified to the level of sp. or morphospecies (Table 2). Demospongiae dominated the assemblage, with high diversity within the Orders Haplosclerida (51 spp.), Poecilosclerida (46 spp.), and Dictyoceratida (35 spp.) (Table A1). Examples of sponges in the region are shown in Figure 3A–J. Some of the morphospecies had many records, e.g., Sarcotragus sp. SS8 has 20 records in the Western Australian Museum, and Halichondria sp. SS1 has 12, potentially indicating these species are commonly encountered in the region and that there is a large quantity of material in museums awaiting further taxonomic study.

Figure 2. Proportional verified records for each taxonomic group of sessile benthic fauna in the four subregions.

Table 2. Total number of verified (V) and unverified (UV) records at the level of family and genera within each faunal group in each study region, along with the total number of verified and unverified records for Ningaloo Reef as a whole and the entire region.

		Ningaloo South		Ningaloo North		Ningaloo Total		Exmouth Gulf		Muiron Islands		Regional Total
		V	UV	V	UV	V	UV	V	UV	V	UV	V	UV
Porifera	Total Families	18	29	47	32	52	40	43	24	23	21	62	45
	Total Genera	26	45	70	40	83	65	76	31	29	20	125	77
	Total Records	44	76	132	91	178	169	247	106	48	64	473	339
Octocorallia	Total Families	11	8	15	10	15	12	19	19	10	13	26	22
	Total Genera	20	11	26	15	30	20	35	29	13	21	55	39
	Total Records	161	36	212	57	373	93	92	128	29	323	494	544
Scleractinia	Total Families	11	11	21	18	21	18	12	10	6	6	22	19
	Total Genera	26	17	66	39	67	40	32	24	8	11	71	45
	Total Records	279	89	930	265	1213	354	227	113	10	30	1450	497
Actinaria	Total Families	1	0	8	1	1	0	2	0	0	0	2	1
	Total Genera	1	0	8	1	1	0	2	0	0	0	3	1
	Total Records	1	0	0	0	1	0	2	0	0	0	3	0
Antipatharia	Total Families	0	0	1	0	1	0	1	2	0	0	1	2
	Total Genera	0	0	1	0	1	0	1	1	0	0	1	2
	Total Records	0	0	1	0	1	0	1	3	0	0	2	3
Cerianthids	Total Families	0	0	1	1	1	1	1	0	0	1	2	2
	Total Genera	0	0	1	1	1	1	1	0	0	1	2	2
	Total Records	0	0	1	1	1	1	1	0	0	1	2	2
Zoanthids	Total Families	4	3	3	3	5	4	4	3	0	1	6	5
	Total Genera	1	0	0	0	1	0	2	0	0	0	2	1
	Total Records	1	0	0	0	1	0	2	0	0	0	3	1
Bryozoans	Total Families	1	0	0	0	1	0	2	0	0	0	3	0
	Total Genera	5	3	4	2	6	3	4	2	0	0	7	4
	Total Records	9	10	8	28	17	38	7	7	0	1	25	46
Corallimorphs	Total Families	3	5	43	27	45	30	7	5	0	0	47	30
	Total Genera	3	5	56	35	59	38	8	7	0	0	64	40
	Total Records	4	16	215	181	219	197	8	13	0	0	227	210
Tunicates	Total Families	2	2	8	0	9	2	12	7	7	1	11	8
	Total Genera	2	2	8	0	10	2	18	10	7	0	22	12
	Total Records	13	4	12	0	25	4	54	31	24	2	103	37
Hydrozoans	Total Families	1	2	7	1	8	3	6	3	2	1	12	7
	Total Genera	1	2	13	1	14	3	17	4	3	1	2	2
	Total Records	1	2	13	1	14	3	17	4	3	1	34	8

Figure 3. Sponges (Photo credits G. Whisson). (A) Caulospongia perfoliata; (B) Cinachyrella australiensis; (C) Cliona celata; (D) Lanthella basta; (E) Xestospongia testudinaria; (F) Gelliodes fibulata; (G) Phyllospongia papyracea; (H) Echinodictyum pulchrum; (I) Trikentrion flabelliforme; (J) Xenospongia patelliformis.

3.2. Octocorallia

One hundred and fifty-nine species of octocorals are recorded from the region (including three species of sea pens). Examples are shown in Figure 4A–E. One hundred and eight of these species were recorded from Ningaloo Reef (Table 1, Figure 2). More octocorals have been collected and recorded from northern Ningaloo (n = 82) than southern Ningaloo (n = 56). Forty-seven species of octocorals have been recorded in Exmouth Gulf to date, including all three identified sea pens, and 20 octocorals have been recorded from the Muiron Islands. Forty-eight percent of the octocoral records were only identified to the morphospecies level (n = 494, Table A1). Some of the species are well represented in museum collections, including Sinularia sp. 5333, which has 15 specimen records, Dendronephthya sp. 5432, which has 14 specimen records, and Sarcophyton sp. 5409, which has 13 specimen records. Some of the more commonly collected/reported soft corals are the Melithaea sea fans, for which there are 74 specimens spread across the Western Australian and Queensland Museums pertaining to at least 11 species, 9 of which are only known at a morphospecies level. Similarly, there are 24 putative species in the region belonging to the genus Sclerophytum; however, 23 of these are known only at the morphospecies level. There are 21 putative Dendronephthya species (Figure 4A); however, 18 of these are only known at the level of morphospecies, and there are 18 putative species of Sinularia in the region, only 2 of which are described (Table A1).

Figure 4. Soft Corals (A–E) and Hard Corals (F–J) (Photo credits A. Hoschke). (A) Dendronephthya sp.; (B) Dichotella gemmacea; (C) Solenocaulon sp.; (D) Latissimia ningalooensis; (E) Sclerophytum sp.; (F) Acropora muricata; (G) Dipsastrea sp.; (H) Duncanopsammia peltata; (I) Plesiastrea peroni; (J) Pachyseris rugosa.

3.3. Scleractinia

Two hundred and forty-seven scleractinian corals are verified to occur in the project area; examples are shown in Figure 4F–J. Two hundred and thirty-nine of these species were recorded at Ningaloo Reef (Table 1, Figure 2), where they accounted for the greatest proportion of species diversity in sessile benthic fauna. The majority of scleractinian corals have been collected from northern Ningaloo (n = 232), with only 65 species being recorded from southern Ningaloo. Fifty-four scleractinian corals have been recorded in Exmouth Gulf to date, and 12 from the Muiron Islands. Amongst the scleractinian corals, there are 48 species of Acropora and 29 species of Montipora (Table A1). Some of the species with the largest number of records are Acropora nasuta, Acropora digitifera, Acropora latistella, Acropora hyacinthus, Acropora millepora, Montipora turgescens, Turbinaria mesenterina, Turbinaria reniformis, Echinopora lamellosa, Pocillopora damicornis, and Cyphastrea serialia. Seventy-four percent of scleractinian coral records are verified (n = 1420, Table 2).

3.4. Actinaria

A total of 23 species of anemone from 15 Families are recorded from the region. Examples are shown in Figure 5A–G. All records come from iNaturalist [30], with no specimens from this region held in museum collections. Thirteen species are reported from Exmouth Gulf, nine from Ningaloo Reef (seven from its northern section), and only one from the Muiron Islands. The most reported anemones are Entacmaea quadricolor (Figure 5F) (Leuckart in Rüppell & Leuckart, 1828) and Heteractis aurora (Quoy & Gaimard, 1833). Several iNaturalist records document new occurrences for the region, including Triactis producta (Klunzinger, 1877), Actinoporus elongatus (Carlgren, 1900), Alicia pretiosa (Figure 5C) (Dana, 1846), and Nemanthus nitidus (Figure 5D) (Wassilieff, 1908), which have not been previously recorded in Western Australia (Rodríguez et al., 2024). Additionally, Actinodendron alcyonoideum (Quoy & Gaimard, 1833) and Dofleinia armata (Wassilieff, 1908) (Figure 5A,B) represent the first documented records for the Ningaloo region.

Figure 5. Anemones (A–G) and Zoanthids (H–K) (Photo credits A. Hoschke) (A) Actinodendron alcyonoideum; (B) Dofleinia armata; (C) Alicia pretiosa; (D) Nemanthus nitidus; (E) Stichodactyla haddoni; (F) Entacmaea quadricolor; (G) Stichodactyla mertensii; (H) Hydrozoanthus gracilis; (I) Palythoa tuberculosa; (J) Zoanthus sansibaricus; (K) Acrozoanthus sp. (undescribed).

3.5. Zoantharia

Twelve species of zoanthids from five families are verified from the study area (Table 1 and Table 2). Examples are shown in Figure 5H–K. Eleven of those species are present on Ningaloo Reef, mainly recorded from the northern section (Table 1). Five species are recorded from Exmouth Gulf, and no records exist from the Muiron Islands. Specimens of four of these species are in the Queensland Museum (Table A1), including Zoanthus sansibaricus (Carlgren, 1900). According to the World List of Zoantharia [35], this species has not been previously recorded in Western Australia. Other records are from iNaturalist and a WAMSI report [25]. One species, Acrozoanthus sp. nov., is known to be new to science but remains undescribed and is currently only reported on iNaturalist. Although it is suspected to represent a new species, the record has not been examined by a taxonomic expert, and a specimen is required before it can be formally described (Figure 5K).

3.6. Bryozoa

Seventy-eight species of bryozoans are verified from the region (Table 1). Examples are shown in Figure 6A–D. Seventy-one of those are recorded from Ningaloo Reef, and the bulk of them are reported from northern Ningaloo (n = 69), with only five from southern Ningaloo. Nine species are from Exmouth Gulf, and no bryozoans have been collected or reported from the Muiron Islands (Table 1). A total of 49 families are represented, with all but nine Bryozoans belonging to the suborder Flustrina. Sixty-three percent of specimens were identified to species level, and most of the collection is held at the Museum of Tropical Queensland. Parasmittina aculeata (Tilbrook, 2006) is not documented in the World Register of Marine Species to occur in Australia [36], and Celleporaria nodulosa (Busk, 1881) (Figure 6A) is not documented in the World Register of Marine Species to occur in Western Australia [36]. There are many specimen records for Stylopoma viride (Thornely, 1905) (n = 42), Cosciniopsis lonchaea (Busk, 1884) (n = 23), suggesting they may be common in the northern section of Ningaloo Reef. Seven of the bryozoan species recorded from Exmouth Gulf have not been collected from Ningaloo Reef.

Figure 6. Bryozoans (A–D), Tunicates (E–H), Hydroids (I–K) (Photo credits G. Whisson). (A) Celleporaria nodulosa symbiotic with anemone; (B) Triphyllozoon sp.; (C) Steginoporella sp.; (D) Caberea sp.; (E) Polycarpa papillate; (F) Botrylloides sp.; (G) Ecteinascidia bandaensis; (H) Didemnum molle; (I) Nemalecium caeruleus; (J) Macrorhynchia philippina; (K) Salacia flavidula.

3.7. Tunicata

A total of 37 species/morphospecies of tunicates representing 12 Families are verified from the region (Table 1 and Table 2). Examples are shown in Figure 6E–H. Most of the specimens are held in the Queensland Museum. The majority (n = 27) are recorded from Exmouth Gulf, whilst 12 species are verified to occur at Ningaloo Reef and 11 are known from the Muiron Islands. Seventy-four percent of records are verified (Table 2), but 14 of the species are only known from iNaturalist records (Table A1). Sigillina cyanea (Herdman, 1899) and Leptoclinides madara (Tokioka, 1953) are well represented with 13 and 12 records, respectively. Some of the iNaturalist species records relate to species that are not known to occur in Australia—e.g., Clavelina amplexa (Kott, 2002), Western Australia—e.g., Ecteinascidia nexa (Sluiter, 1904), or in the Pilbara region—e.g., Perophora modificata (Kott, 1985) according to the Ascidiacea World Database (Shenkar et al., 2024).

3.8. Hydrozoa

Fifteen hydrozoans were recorded across the region (Table 1). Examples are shown in Figure 6I–K. The species with the most records is Macrorhynchia philippina (Kirchenpauer, 1876) (Table A1). Nine species are known from Ningaloo Reef, six are only recorded from Exmouth Gulf, and one is only known from the Muiron Islands. Nine of the species are represented only by iNaturalist records (Table A1). Several of the iNaturalist records represent new records for Australia, including Nemalecium caeruleus (Galea and Maggioni, 2024) and Dentitheca habereri (Stechow, 1909). The observations of Salacia flavidula (Figure 6K) (Watson, 2000) and Solanderia secunda (Inaba, 1892) in Exmouth Gulf represent new records for Western Australia and for the region.

3.9. Other Anthozoa: Antipatharia, Ceriantharia, and Corallimorpharia

Few verified records exist for these taxa, with the Antipatharia only represented by three species and Ceriantharia and Corallimorpharia are represented by two species each (Table 1). All these species are only identified at a genus level; their species-level identity is not known (Table A1). Two of the three black corals are only recorded from Exmouth Gulf, with the other present in southern Ningaloo Reef. One tube anemone is only known from Exmouth Gulf, and the other is recorded from northern Ningaloo Reef. One corallimorph is known only from Exmouth Gulf, and the other is recorded at both northern Ningaloo and the Muiron Islands. No specimens of corallimorphs or tube anemones occur in Australian Museums, and these records pertain to iNaturalist observations only.

4. Discussion

Our study reveals a remarkable diversity of sessile benthic invertebrates in waters shallower than 30 m across the Gascoyne southern Pilbara region. By consolidating specimen-based museum records with data from the Atlas of Living Australia, we identified a total of 827 species or morphospecies. Notably, Ningaloo Reef boasts the highest diversity, with 586 species, including 239 species of scleractinian corals and 123 species of sponges. The northern section of Ningaloo Reef (north of Point Cloates) accounts for 510 species, whereas the southern section has only 185 species; 295 species recorded occur in Exmouth Gulf, including 125 sponges, 17 tunicates, and 18 anemone species that are not found in neighboring regions. In contrast, the Muiron Islands show a striking lack of data, with just 86 species confirmed.

4.1. Updating Diversity Estimates for Ningaloo Reef and the Muiron Islands

Previous studies report that over 200 coral species and 155 sponge species inhabit the shelf, slope, and deep-sea environments of Ningaloo Reef [31]. Our study substantially updates these estimates, confirming that 239 scleractinian corals, 124 sponges, and 108 species of soft corals (including Latissimia ningalooensis, Ekins, Benayahu & McFadden, 2022, see Figure 4D, which was described from specimens collected at Ningaloo Reef) occur in shallow habitats (to 30 m depth). At least 113 other invertebrates are recorded from Ningaloo Reef, including bryozoans (71 spp.), tunicates (12 spp.), zoanthids (11 spp.), anemones (10 spp.), hydrozoans (9 spp.), and black corals, corallimorphs, and cerianthids (1 sp. each). Taken together, we estimate that at least 587 species of sessile marine invertebrates inhabit Ningaloo Reef.

A notable scleractinian coral record from Ningaloo Reef is the single specimen of Acropora bushyensis from the northern sector. This specimen is housed in the Museum of Tropical Queensland collection but is not included in The Corals of the World Database [37], which reports this species from Shark Bay but not Ningaloo Reef. Sponge records of biogeographic interest from Ningaloo Reef include Sigmaxinella soelae (Hooper, 1984) and Ceratopsion montebelloenses (Hooper, 1991), which are regional endemics only known from the Pilbara, and Corticium monolophum (Sarmento, Lage, Almeida & Fromont, 2021), which is endemic to Western Australia. Many of the verified and named sponge species recorded in this study are not listed as occurring in the region in the World Porifera Database [38]. For example, Desmapsamma vervoorti (van Soest, 1998) and Liosina granularis (Kelly-Borges & Bergquist, 1988) are not reported from Australia. Callyspongia manus (Lendenfeld, 1887) is not reported from Western Australia, and Teichonopsis labyrinthica (Carter, 1878) and Biemna saucia (Hooper, Capon & Hodder, 1991) are not listed as occurring on Ningaloo Reef. Such discrepancies highlight that online databases do not always capture specimen-based records, particularly when data are not easily accessible, emphasizing the value of developing integrated approaches to consolidate and standardize datasets to support future taxonomic and biogeographic research.

The Muiron Islands are considered separately from Ningaloo Reef in this study due to their distinct zoning structure and environmental conditions. Even though the sessile marine invertebrate fauna of the Muirons remains substantially under-sampled, it is notable that 22 species of sponges, 14 species of octocorals (including Chromonephthea muironensis (van Ofwegen, 2005), which was originally described from the Murion Islands), along with five species of tunicates that were recorded, are absent from Ningaloo Reef. Previous studies have also reported a higher abundance of soft corals at the Muiron Islands compared to Ningaloo Reef [11]; however, we cannot verify that with this dataset.

4.2. Unique Fauna of Exmouth Gulf

We estimate that Exmouth Gulf hosts at least 295 species, marking the first recorded estimate of sessile invertebrates for this location. Importantly, 165 of these species are not found at Ningaloo Reef or the Muiron Islands, suggesting they may be unique to Exmouth Gulf and adapted to turbid water conditions. Among these records are 125 sponges, 54 hard corals, 47 soft corals (including all three sea pen species not found at Ningaloo Reef or the Muiron Islands and Chromonephthea bundegiensis (Verseveldt, 1977 which was described based on specimens from the Gulf), 27 tunicates, 18 anemones, and 9 bryozoans. One scleractinian coral of particular interest is Acropora kosurini, which was only recorded in Exmouth Gulf. There are two specimens of this coral in the Museum of Tropical Queensland collection; however, Veron et al. [37] indicate this species does not occur in Australia. Another species of interest is Micromussa pacifica, which was described in [39]; however, no specimens from the region exist in Australian collections at present, and it is only known from Exmouth Gulf based on photographic records. Given the unique environmental conditions in Exmouth Gulf, the finding of a unique assemblage featuring novel sea pens, sponges, tunicates, and anemones demonstrates the likelihood that unique environmental conditions drive benthic assemblage composition and diversity and create distinctly unique communities.

4.3. Taxonomic and Spatial Gaps

The diversity estimates provided in this study are likely to be significant underestimations. Global and Australian marine biodiversity studies indicate that between one-third and two-thirds of marine species remain undescribed [40,41]. Our study reinforces that estimate because 41% (n = 341) of the verified sessile marine invertebrate fauna in the project area are classified at the level of morphospecies. Including morphospecies was essential to this study, given that many sponges (64%, n = 161) and soft corals (74%, n = 115) are only identifiable at this level. Applying Linnean names to morphospecies already identified as distinct taxa should be prioritized. An additional priority is to collect specimens of those species known only from iNaturalist records, particularly anemones, corallimorphs, zoanthids, cerianthids, and hydrozoans, to confirm those records and advance the taxonomy of these groups.

It is also recommended that further taxonomic studies be undertaken on the thousands of unverified records related to specimens in Australian museums that have only been identified to higher taxonomic levels. The records treated as “unverified” include but are not restricted to 176 sponges in the collections of the WAM and QM, 80 scleractinians spread across the WAM, QM, and MTQ collections, as well as 71 soft corals and 56 bryozoans in the MAGNT and MTQ collections. All this museum-accessioned material is available for study (see ESM1 for source information), and we recommend prioritizing these existing resources for taxonomic and systematic research, as many specimens may represent new species or be endemic to the region. It is also recommended that similar synthesis and gap analyses studies should be undertaken for other sessile, motile, and pelagic marine invertebrate fauna such as molluscs, echinoderms, crustaceans, ctenophores, siphonophores, and scyphozoans, where similar reservoirs of unidentified material are likely to exist in museums.

There are relatively few faunal records for marine invertebrates from the Muiron Islands and the southern sector of Ningaloo Reef, likely due to limited survey efforts in these areas rather than due to lower benthic invertebrate diversity. To gain a more comprehensive understanding of regional diversity patterns, it is recommended to conduct additional diversity surveys in these locations, as well as in Exmouth Gulf. Furthermore, it is surprising to find discrepancies between the spatial distribution data in the Atlas of Living Australia and the global diversity databases maintained by the World Register of Marine Species [32], such as the World Porifera Database [38] and the World List of Zoantharia [35]. Ongoing efforts to consolidate and align this information would greatly enhance the interpretation of species ranges and help detect future range expansions and contractions.

4.4. Future Directions for Research

Although species records provide valuable information, they should not be interpreted as direct measures of abundance, as most specimens were collected across multiple projects with different objectives and sampling strategies. Consequently, the data reflects opportunistic collections with inherent biases that preclude a direct assessment of community ecology. Accurate quantification of taxon abundance and site-level diversity requires replicated systematic surveys. Such ecological data would improve our understanding of community structure and responses to a warming ocean, particularly for hard corals under unprecedented recent thermal stress and for soft corals at the Muiron Islands, which may serve as a regional refugium. Establishing robust baseline biodiversity data about habitat-forming benthic invertebrates in natural and artificial habitats (e.g., King Reef, Navy Pier) is similarly critical, as these species provide food and habitat for a diverse range of vertebrates and invertebrates, often serving as nurseries for juvenile fish [18]. Building comprehensive ecological datasets will enable assessment of both natural benthic diversity and the role of artificial habitats in supporting regional biodiversity.

Ningaloo reefs have proven susceptible to past thermal stress events (2011 and 2013) [42,43], and corals in Ningaloo and surrounding regions (Pilbara, Kimberley) were severely impacted by the 2024–2025 heatwave [44]. One study predicted that the corals of Ningaloo Reef will be vulnerable to future climate change, as their genetic signatures indicated they will need to undergo substantial and rapid adaptive shifts to keep pace with ocean warming, highlighting that Ningaloo Reef coral communities may face a significant risk of diversity loss under future climate scenarios [45]. Similarly, light-limited coral communities in Exmouth Gulf, which are characterized by elevated turbidity, may also be vulnerable to future climate stressors and bleaching because they have lower growth rates and reduced reproductive fitness compared to neighboring clear-water communities [46].

The region has also faced major natural disturbances, including Category 5 Cyclone Vance in 1999 and Cyclones Hamish (2009), Narelle (2013), and Seroja (2021), all of which caused substantial physical damage to marine habitats [47]. Outbreaks of coral-eating Drupella snails, with densities reaching 175 m² in 1985, have also led to severe localized coral cover declines [48]. Ningaloo Reef, particularly Bills Bay at Coral Bay, has experienced two significant deoxygenation events: the first in 1989 [49] and the second in 2022, when live coral cover plummeted from 70% to 1% due to trapped coral spawn causing eutrophication and asphyxiation of marine life [50].

The absence of long-term monitoring of diversity, abundance, and health at the Muiron Islands and Exmouth Gulf leaves a critical gap in understanding the cumulative impacts of stressors in these regions. Expanding and funding monitoring programs, conducting targeted ecosystem health and diversity assessments, and obtaining contemporary estimates of abundance are recommended as key priorities for the region to improve ecosystem management. Complementing these efforts with taxonomic research on existing specimens and integrating specimen-based records across national and global biodiversity and taxonomic databases will enhance future biogeographic and ecological research and provide a more complete understanding of regional biodiversity and ecosystem change under a rapidly warming ocean.