Publications
Healing country together: A seagrass restoration case study from Gathaagudu (Shark Bay)
A successful seagrass restoration project in Shark Bay, Western Australia, demonstrates the power of integrating Western science with Indigenous traditional ecological knowledge. The partnership, involving the Malgana Aboriginal Corporation Ranger program, facilitated two-way knowledge sharing through On Country workshops, leading to effective restoration methods tailored for Gathaagudu. This collaboration not only restored seagrass ecosystems but also fostered cultural education, language preservation, and a deeper connection between people and their environment. The study highlights the potential of such partnerships to address long-standing restoration challenges while promoting holistic healing for both people and Country.
Assessing the Influence of HGT on the Evolution of Stress Responses in Microbial Communities from Shark Bay, Western Australia
Research at Shark Bay, Western Australia, reveals that horizontal gene transfer (HGT) has played a significant role in the evolution of stress response mechanisms in microbial communities inhabiting pustular mats. These mats serve as modern analogs of ancient microbial systems and are subject to various environmental stresses such as osmotic stress, oxidative stress, and arsenic toxicity. Using the MetaCHIP tool, scientists identified HGT events related to stress response genes in 83 metagenome-assembled genomes. Phylogenetic analyses suggest that these gene transfers may have occurred outside modern pustular mats, indicating a potentially long history of HGT. Notably, a specific osmoprotectant transport gene shows recent adaptations, hinting at interactions between Planctomycetota and Myxococcota within the mats. The findings underscore the ongoing microbial adaptations and evolution in these unique ecosystems.
Bidirectional fabric evolution in Hamelin Pool microbialites, Shark Bay, Western Australia
Researchers at Shark Bay, Western Australia, have uncovered bidirectional fabric evolution in microbialites within Hamelin Pool, revealing that these structures evolve both upward and downward as they grow. The study identified four accretionary mat types—pustular, smooth, colloform, and transitional—and demonstrated that while the surface mats change with water depth, subsurface microfabrics undergo a taphonomic progression from depositional architecture to micritic thickening and cement infilling. This bidirectional evolution suggests microbialites are not solely products of accretionary mat types but also result from early lithification processes, potentially enhancing their preservation in the geological record. The findings were derived from mesoscale and microscale observations, including polished slabs, thin section scans, optical microscopy, scanning electron microscopy, and energy-dispersive X-ray spectroscopy.
Little change in surface sediment carbon stock following seagrass restoration in Shark Bay, Western Australia
A study on seagrass restoration in Shark Bay, Western Australia, reveals that surface sediment carbon stocks show little to no recovery up to five years after the restoration of Posidonia australis. Despite efforts to restore seagrass meadows, organic carbon concentrations and isotopic signatures (δ13C) in newly restored areas remained statistically indistinguishable from unvegetated sand. This suggests that carbon sequestration capacity does not return quickly even with successful seagrass reestablishment. The findings highlight the slow recovery of sediment carbon stocks following restoration efforts, with potential implications for climate change mitigation strategies relying on seagrass restoration.
Metagenomic, (bio)chemical, and microscopic analyses reveal the potential for the cycling of sulfated EPS in Shark Bay pustular mats
Research at Shark Bay, Western Australia, reveals that sulfated extracellular polymeric substances (EPS) play a significant role in microbial interactions and carbon cycling within ancient peritidal pustular mats. Metagenomic analysis identified cyanobacteria as the primary producers of these sulfated polysaccharides, while enzymes like sulfatases and glycosyl hydrolases, detected across multiple bacterial clades, indicate active degradation processes. Biochemical and microscopic analyses confirmed that sulfur abundance correlates with cyanobacterial presence, suggesting a dynamic cycle of synthesis, modification, and degradation that influences biomineralization and microbial community structure.
The microbial carbonate factory of Hamelin Pool, Shark Bay, Western Australia
Hamelin Pool, located in Shark Bay, Western Australia, functions as a modern microbial carbonate factory, offering critical insights into sedimentary deposits of microbial origin found in the geologic record. This study reveals that while the pool is renowned for its living marine stromatolites, erosion and degradation of weakly lithified microbial mats significantly contribute to the production and accumulation of sand-sized micritic grains. Comprehensive mapping shows that over 40 km² of upper intertidal shoreline and 20 km² of subtidal pavements are colonized by these mats, which erode to form irregular peloidal grains and platey micritic intraclasts. Together, these sediments make up nearly 26% of the total sediment in the pool, plausibly producing around 24,000 metric tons annually. This dual process of construction by lithifying microbial mats and erosion of weakly lithified mats provides a modern analog for ancient microbialite-micritic sediment facies associations.
Depositional timing and palaeoclimate interpretation of the Tamala Limestone aeolianites in Shark Bay, Western Australia
Paleoclimate reconstructions of Shark Bay reveal that the Tamala Limestone, a vast aeolian carbonate system along Western Australia's coast, was shaped by alternating glacial and interglacial intervals during the Pleistocene. Amino acid dating indicates units age eastward, while sedimentary breaks correlate with interglacial paleosols, suggesting prolonged aridity during glacial periods due to weakened Leeuwin Current and northward shifts in atmospheric circulation cells. This study combines stratigraphic and sedimentological analyses to demonstrate that lower sea levels and cooler Indo-Pacific Warm Pool temperatures coincided with drier conditions, while humid interglacials facilitated carbonate dissolution and paleosol formation.
Genome-resolved metagenomics provides insights into the functional complexity of microbial mats in Blue Holes, Shark Bay
A groundbreaking study reveals the functional complexity of microbial mats in Shark Bay's Blue Holes, uncovering diverse and potentially novel microorganisms, including members of DPANN, Asgard archaea, and candidate phyla radiation. These mats, thriving in hypersaline conditions, exhibit unique metabolic pathways, such as photoheterotrophy, and harbor a range of putative rhodopsins with uncharacterized functions. The research employed high-throughput metagenomic sequencing and hyperspectral confocal microscopy to analyze 117 medium- to high-quality metagenome-assembled genomes, identifying critical microbial interactions, viral defense mechanisms, elemental transport, osmoprotection, heavy metal resistance, and UV resistance. This study significantly enhances our understanding of these distinct mat systems and their adaptive responses.
Structure and function of Shark Bay microbial communities following tropical cyclone Olwyn: A metatranscriptomic and organic geochemical perspective
Tropical cyclones significantly alter microbial communities and geochemical processes in Shark Bay, Western Australia. Following Cyclone Olwyn (2015), black sludge deposits formed between microbialite columns, dominated by heterotrophic and anaerobic microbes like methanogens and sulfate-reducing bacteria. These microbes drove calcium carbonate precipitation, aiding mat preservation. Organic geochemical analysis revealed elevated C25 highly branched isoprenoid (HBI) alkenes, linked to cyclone-induced relocation of subtidal sediments containing HBI-producing diatoms. Additionally, sulfur-bound hopanoids and benzohopanes in mucilaginous cobbles suggested microbial matter influenced by cyclone-driven anoxia, promoting organic sulfurization. The study used metatranscriptomic and GC-MS analyses to uncover these post-cyclone changes.
A trial of transmitter attachment methods for Shark Bay bandicoots (Perameles bougainville)
Research on Shark Bay bandicoots (Perameles bougainville) demonstrates that collars, when fitted under general anaesthetic, provide the most effective and welfare-friendly method for monitoring these animals during reintroduction programs. The study found that collared bandicoots could be tracked for up to seven weeks with minimal harm, addressing a key challenge in post-release monitoring where alternative attachment methods often result in significantly shorter tracking durations.
Abundance estimates of Southern Hemisphere Breeding Stock ‘D’ humpback whales from aerial and land-based surveys off Shark Bay, Western Australia, 2008
Aerial and land-based surveys conducted off Shark Bay, Western Australia, in 2008 estimated the abundance of northward-migrating Southern Hemisphere Breeding Stock 'D' humpback whales at 34,290 (95% CI: 27,340–53,350), marking a 12.9% annual rate of increase since a 1999 estimate of 11,500. The study utilized single-platform aerial line transect and land-based surveys from Cape Inscription, Dirk Hartog Island, during the peak migration period (8–20 July). Practical challenges reduced the effectiveness of dual-survey approaches for estimating g(0), leading to alternative methods yielding higher estimates (around 0.6–0.7) and a conservative abundance estimate of 17,810 (14,210–27,720). The findings highlight significant growth in the population but also underscore methodological limitations in dual-survey techniques.
Discovery of an Abundance of Biosynthetic Gene Clusters in Shark Bay Microbial Mats
Researchers have uncovered a remarkable abundance of biosynthetic gene clusters (BGCs) in the microbial mats of Shark Bay, Western Australia. This discovery highlights the potential for microorganisms in extreme environments to produce secondary metabolites, which offer competitive advantages and biotechnological applications. The study identified 1477 BGCs across a 20 mm depth horizon, with the surface layer showing the highest relative abundance. Notably, terpene and bacteriocin BGCs were prominent, suggesting their significant roles in ecosystem function. Additionally, potentially novel BGCs were detected in Heimdallarchaeota and Lokiarchaeota, archaeal phyla not previously known to possess such clusters. This finding provides new insights into how secondary metabolites may enable microbial communities to adapt to harsh conditions.
Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses
Microbial mats in Shark Bay, Western Australia, exhibit strong adaptive responses to hypersaline conditions, with gene transcription influenced by community structure and seasonality. The study reveals that these mats prioritize nutrient uptake—particularly fatty acids, phosphorus, iron, and nickel—and employ protective mechanisms against salinity and ammonium buildup. Key pathways for carbon cycling include anoxygenic photosynthesis and chemoautotrophy via the Arnon-Buchanan cycle, while smooth mats show enrichment in anaerobic processes like sulfate reduction and methanogenesis, reinforcing their role as modern analogs to ancient microbialites. This first metatranscriptomic analysis of actively growing hypersaline mats provides insights into their metabolic resilience and ecological significance.
Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes
A groundbreaking metagenomic analysis of Shark Bay's microbial mats reveals the functional complexity underlying its biogeochemical cycles, particularly carbon fixation via the Wood–Ljungdahl pathway. The study identified 87 medium-to-high-quality metagenome-assembled genomes (MAGs), including novel bins under the Asgard archaeal groups Thorarchaetoa and Lokiarchaeota. Key pathways for sulfur, nitrogen, phosphorus cycling, and environmental adaptation—such as UV resistance, hypersalinity tolerance, and heavy metal resistance—were mapped at a millimeter scale using shotgun sequencing on the Illumina NextSeq 500 platform. Over-representation of genes like those for sulfate assimilation, methanogenesis, and polyhydroxyalkanoate (PHA) synthase suggests specialized carbon storage and microbial interactions. The research also highlights putative viral defensive mechanisms, offering new models for how biogeochemical processes and adaptive responses partition in these extreme environments.
New multi-scale perspectives on the stromatolites of Shark Bay, Western Australia
A recent intensive field program at Shark Bay, Western Australia, has revealed that coccoid cyanobacteria, not filamentous ones, dominate the microbial mats forming lithified stromatolite buildups, contradicting traditional views. This discovery was enabled by multi-scale mapping and molecular studies, which identified eight distinct 'Stromatolite Provinces' with unique geographic distributions of stromatolite structures. Additionally, analysis of internal fabrics showed pervasive microcrystalline carbonate precipitation in microbial mats, suggesting parallels with Precambrian stromatolites. These findings advance our understanding of benthic ecosystems on early Earth and provide a foundation for further studies on stromatolite morphogenesis.
Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics
Shark Bay's hypersaline microbial mats, potential analogues of Earth's earliest ecosystems, exhibit unique metabolic pathways not found elsewhere. A first-of-its-kind shotgun metagenomic analysis revealed that these mats are dominated by Proteobacteria, Cyanobacteria, and Bacteroidetes, with distinct microbial community structures compared to Highbourne Cay (Bahamas). Notably, Shark Bay mats feature alternative non-rubisco-based carbon metabolism pathways, such as the reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate cycles, which are absent in other studied ecosystems. Additionally, evidence suggests novel nitrogen and heavy metal cycling processes involving arsenic, mercury, copper, and cadmium. Archaea, highly represented here, may play critical roles in ecosystem function, highlighting Shark Bay's microbial mats as unique and complex ecosystems warranting further study.
Carbon, nitrogen and phosphorus storage in subtropical seagrass meadows: examples from Florida Bay and Shark Bay
Seagrass meadows in Florida Bay and Shark Bay, Western Australia, store significant amounts of organic carbon and nutrients, with Shark Bay soils containing 21% more organic carbon and 35% more phosphorus than those in Florida Bay. Shark Bay also exhibits lower soil density, indicating a less compacted structure. Hypersaline regions in both bays show higher surficial soil organic carbon content. While Florida Bay's soil profiles suggest increased phosphorus delivery and primary productivity over the past century, Shark Bay's profiles indicate a decline in these factors over the last 1000 years. Despite differences, both bays rank among global hotspots for coastal ecosystem organic carbon storage, with Shark Bay storing an average of 243.0 MgCorg ha⁻¹ compared to Florida Bay's 163.5 MgCorg ha⁻¹.
Characteristics, distribution and morphogenesis of subtidal microbial systems in Shark Bay, Australia
Extensive subtidal microbial deposits, covering approximately 300 km² of Hamelin Pool in Shark Bay, Australia, have been mapped and analyzed for the first time. These deposits, dominated by aragonite with distinctive isotopic signatures (δ13C +4.46 to +5.88; δ18O +3.06 to +3.88), reveal a subtidal microbial habitat 10 times larger than previously known intertidal areas. The study highlights two depositional stages, with growth rates ranging from <0.1 mm/year to 0.5 mm/year, and provides evidence of late Holocene sea-level changes through fabric sequences. Distinct microbial communities and lateral fabric relations were identified, emphasizing the geoscientific significance of Hamelin Pool for early life studies and ancient environmental interpretations.
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