Journal of the Royal Society of Western Australia, 101: 17-43, 2018 Microbiomes of Western Australian marine environments CHARLIE M. PHELPS1, RACHELE BERNASCONI1, MELISSA DANKS2, JOSEP M. GASOL13, ANNA J. M. HOPKINS2, JACQUELYN JONES4, CHRISTOPHER R. J. KAVAZOS25, BELINDA C. MARTIN6, FLAVIA TARQUINIO1, MEGAN J. HUGGETT127* 1 Centre for Marine Ecosystems Research, and2 Centre for Ecosystem Management, School of Science, Edith Cowan University. Perth, WA, Australia 3 Institut de Ciencies del Mar, CSIC. Barcelona, Catalonia, Spain 4 Trace and Environmental Laboratory, Curtin University. Perth, WA, Australia 5 School of Biological, Earth and Environmental Sciences, The University of New South Wales. Sydney, NSW, Australia 6 School of Biological Sciences, The University of Western Australia. Perth, WA, Australia 7 School of Environmental and Life Sciences, The University of Newcastle. Ourimbah, NSW, Australia *Corresponding author:i;W [email protected] Abstract Microbes are fundamentally important to the maintenance of all habitats, including those in the ocean: they govern biogeochemical cycles, contribute to resistance from disease and nutritional requirements of macroorganisms and provide enormous biological and genetic diversity The oceanic environment of the west coast of Australia is dominated by the Leeuwin Current, a poleward flowing boundary current that brings warm water down the coastline from the north. Due to the influence of the current, tropical species exist further south than they would otherwise, and stretches of the coastline host unique assortments of tropical and temperate species. Seawater itself, as well as the benthic macroorganisms that inhabit ocean environments, form habitats such as extensive areas of seagrass beds, macroalgal forests, coral reefs, sponge gardens, benthic mats including stromatolites, continental slopes and canyons and abyssal plain enviroments. These environments, and the macroorganisms that inhabit them, are all intrinsically linked with highly abundant and diverse consortiums of microorganisms. To date, there has been little research aimed at understanding these critical organisms within Western Australia. Here we review the current literature from the dominant coastal types (seagrass, coral, temperate macroalgae, vertebrates and stromatolites) in Western Australia. The most well researched are pelagic habitats and those with stromatolites, whereas data on all the other environments are slowly beginning to emerge. We urge future research efforts to be directed toward understanding the diversity, function, resilience and connectivity of coastal microorganisms in Western Australia. KEYWORDS: Marine microbiome. Western Australia, coral, seagreass, bacterioplankton, macroalgae Manuscript received 24 July 2018; accepted 15 November 2018 INTRODUCTION The term ‘microbiome’ (from ‘microbe’ and ‘biome’) refers to the microbes living on a specific habitat, In terms of both abundance and diversity, all ecosystems e.g., the ocean microbiome, which includes the water on Earth are dominated by microbes which, although microbiome, the sediment microbiome, the microbiome invisible to the naked eye, are essential for the of macroalgae, seagrasses, corals and sponges, as well functioning of the biosphere. We collectively refer as the microbiomes of marine fish and marine mammals. to prokaryotes (bacteria and archaea), microscopic The microbiome also refers to the total genomic pool of the eukaryotes (such as protists and fungi) and viruses as microbiota. In host-associated microbiomes, this extends "microbes", all of which are abundant in every aquatic the host’s functional genome well beyond its evolutionary environment. The global ocean prokaryotic biomass capabilities. alone is in the order of a petagram of carbon (1015 grams), In addition to their enormous abundance, microbial with ocean sediment harbouring up to ten times more than this (Whitman et al., 1998). Microbes also colonise communities harbour a vast metabolic functional diversity to obtain energy from oxidation-reduction biotic and abiotic surfaces in the marine environment chemical reactions including photosynthesis. As a to form complex biofilm communities, and proliferate consequence, prokaryotes are essential to fulfilling many in the tissues of many marine organisms, performing biogeochemical roles, and are likely to be responsible for ecological functions essential to their hosts (see pull-out box, microbiomes Egan et al., 2008). most, if not all, key transformations in global cycling of carbon, nitrogen, phosphorus, sulphur and iron. About half of the Earth's primary production (i.e. the conversion © Royal Society of Western Australia 2018 of atmospheric C02 into organic substances within living 17 Journal of the Royal Society of Western Australia, 101, 2018 organisms) is in the ocean, with most of this (ca. 90%) 2015 and Sweet & Bulling, 2017). In addition, the large performed by microbes (Duarte & Cebrian, 1996; Field genomic diversity within oceanic microbes has a large et al., 1998). In addition, most of the global respiration biotechnological potential (Arrieta et al., 2010; Arnaud- (i.e. the degradation of organic carbon into C02) stems Haond et al., 2011). Hence, there is a vital need to improve from microbial processes (del Giorgio & Duarte, 2002). our understanding of the diversity, function, resilience This productivity sustains marine food webs and is and connectivity of microorganisms in the ocean. fundamental to many of the services of the world's oceans. MICROBIOMES OF WESTERN Understanding the diversity and ecology AUSTRALIA of microbiomes has been facilitated by the recent development of 'omic' approaches. These methodologies With more than 20 000 km of coastline (of which 12 000 are based on the cost-effective sequencing of either correspond to the mainland and the rest to islands). the whole DNA of the community (metagenomics), Western Australia has an estimated >300 000 km2 of the whole mRNA (metatranscriptomics) or various territorial waters, mostly over the continental shelf. taxonomic marker genes that are amplified before Under the Integrated Marine and Coastal Regionalisation sequencing (typically the 16S rDNA for prokaryotes and of Australia, this area can be divided either into several the 18S rDNA for eukaryotes). Despite this explosion large Provincial Bioregions, or into eighteen mesoscale of sequence-based data and the dominance in both Bioregions (Fig. 1). Transitional zones, or biotones, are abundance and diversity of microbes in oceans, we represented by the bioregions located between provincial understand relatively little of their population dynamics, water types and signify areas where species likely exist metabolic complexity and synergistic interactions at the limit of their distributions. Three provincial zones with macro-organisms. There is mounting evidence and four associated biotones are represented along that the health of many marine organisms depends on the Western Australian Coast. There are 18 defined their associated microbiome (e.g., Zozaya-Valdes et al., bioregions located along the Western Australia coast. Meso-scale Bioregions OSS - Oceanic Shoals BON - Bonaparte Gulf CAB - Cambridge-Bonaparte KIM - Kimberley KSD - King Sound CAN - Canning EMB - Eighty Mile Beach PIO - Pilbara (offshore) PIN - Pilbara (nearshore) NWS - North West Shelf NIN - Ningaloo SBY - Shark Bay ZUY - Zuytdorp ABR - Abrolhos Islands CWC - Central West Coast LNE - Leeuwin-Naturaliste WSC - WA South Coast EUC - Eucla Provincial Bioregions | | Tropical Waters [ | Subtropical Waters | | Warm Temperate Waters Transitional Waters 200 0 200 400 600 800 km Figure 1. Location of Integrated Marine and Coastal Regionalisation for Australia (IMCRA) Provincial and Meso-scale Bioregions for the Western Australian Coast. Data Source: Commonwealth of Australia (2006). The warm southward flowing Leeuwin Current is represented by blue arrows. 18 C. M. Phelps et ah: Microbiomes of Western Australian marine environments 10 of which are located within the tropical waters of continents such as America or Africa. This creates unique the Northwest Province and Northwest Transition (Fig. subtropical conditions that extend towards relatively high 1). Across this large range of latitude (> 20° of latitude southern latitudes. Additionally, the Leeuwin Current from ca. 14°S to 36°S) average sea surface temperatures generates warm-core and cold-core eddies, the former (SST) vary from 28°C in the north to 17°C in the south. often entrapping productive shelf waters and creating In addition, the Western Australian coast ranges from a mosaic of waters with differences in temperature, sandy microtidal sites in the southernmost parts, to phytoplankton and productivity (Waite et ah, 2007; structurally complex macrotidal environments in the Paterson et ah, 2013). north where there is a significant effect of shallow reefs In addition to the oceanographic dynamics the shelf is and island archipelagos that create structure and small- very extensive in some regions (particularly in the north) scale variability. with morphologically complex structure of shallow Within Western Australian waters, a number of key water habitats (Jones et ah, 2014). There are steep canyons ecological features have been identified that are expected that connect the shelf with deep ocean. In particular the Perth Canyon near the Rottnest Island in the Leeuwin- to affect the distribution and activity of microbes. Naturaliste Bioregion (Fig. 1), allows episodic upwelling Both the pelagic and benthic environments of Western Australia are conditioned by the water current that of nutrient-rich deep waters. Inshore lagoons are key transports warm tropical Indian Ocean waters along sites of high benthic productivity (including macroalgae the coast, i.e. the Leeuwin Current that flows parallel and seagrass). These lagoons support diverse and to the coast from north to south and continues east endemic invertebrate and vertebrate species that include after encountering Cape Leeuwin in the southwestern commercial and recreational species of migratory fish. most extremity of the continent. In the South Australian Finally, in the coastal regions of Western Australia are Bight the Leeuwin Current is cooler as it is affected by highly diverse, living stromatolites of various ages that the Antarctic Circumpolar Current from the west and hold extraordinary evolutionary significance (Gudhka et is compressed towards the coast. In addition to these ah, 2015). main currents, the Holloway Current in the north flows We chose to focus this review on a variety of parallel to the northern Western Australian coastline and microbiomes that reflect the importance of these Western along the shelf, transporting warm, low salinity waters Australian ecological features and the availability of from the Arafura Sea and Gulf of Carpentaria into the published literature (Fig. 2). These microbiomes include: Leeuwin Current. As the Holloway Current also flows seagrass, coral, temperate macroalgal, vertebrate, benthic parallel to the coast in the northern part of the coastline, mats and stromatolites and planktonic (free-living) it in part pushes the Leeuwin Current towards the microbiomes (Fig. 3). In general, we have restricted coast. As a result, these warm waters found at southern our review to shallow waters, given the comparatively latitudes in Australia's west coast set this coast apart from higher amount of research that has been focussed on the oceanographic dynamics of the west coasts of other shallow benthic systems versus deeper oceanic settings (a) (b) SO | Plankton 0 | Stromatolite jrfhfc J 40 Benthos (microbial mat) | Seagrass ] Coral 8 30 |j Macroalga ^ Vertebrate | 20 10 1900-69 1970-79 1980-89 1990-99 2000-2009 2010-2016 Decade Figure 2. Number of journal articles published on marine microbes in Western Australia showing a) host/habitat they were from, and b) the decade they were published. A list of the references used in this figure are provided in Appendix 1. Symbols from the Integration and Application Network (ian.umces.edu/symbols/). 19 Journal of the Royal Society of Western Australia, 101, 2018 A SEAGRASSES A CORAL A MACROALGA a 0081 008 A VERTEBRATE A STROMATOLITES A PLANKTON 008^ ) o 1 Nutrient cycling (i.e. sulphur, phosphate, nitrogen) Growth support (i.e. phytohormones) Jf Protection (i.e. antimicrobial & antifungal, occupation of niches) Horizontal/beneficial gene transfer w fq Symbiosis 0! Primary producers Structure formation Decomposition/spoilage Figure 3. Conceptual diagram of Western Australian microbiomes and the functional roles that microbial communities play within each habitat. Symbols are from the Integration and Application Network (ian.umces.edu/symbols/). in Western Australia. There are also a variety of other Seagrass microbiomes habitats and organisms (e.g., salt marshes, mangroves or Seagrasses are marine flowering plants (angiosperms) invertebrates such as sponges, molluscs and arthropods) that are distributed along the coastlines of every that are not included in our review due to scarcity continent except Antarctica (Short et al., 2007). Seagrasses of data, even though we recognise that these are also can be referred to as 'ecosystem engineers' (see pull-out important components of the marine ecosystem. As it box, page 21; Jones et al., 1994); they provide a multitude will become clear, the microbial ecology of the oceans of ecosystem services such as coastal protection surrounding Western Australia is poorly understood. We from erosion (Ackerman & Okubo, 1993), sediment postulate that a full understanding of life in the ocean stabilisation (Gacia & Duarte, 2001) and represent a requires knowledge of the microbial taxa, their genomes, habitat and source of food for a variety of organisms functioning, biogeographical patterns, and synergistic (Staples et al, 1985; Heck et al., 2008; Bertelli & Unsworth, associations to themselves and larger eukaryotic hosts. 2014). Seagrasses also sequester and store an estimated A research agenda including these subjects will benefit 19.9 Pg of organic carbon, (roughly 10-18% of the total our understanding of the oceanic environments and oceanic carbon sequestration; Fourqurean et al., 2012; will facilitate development of techniques to be used as Lavery et al., 2013; Serrano et al., 2016). health diagnosis tools for both ocean organisms and environments. 20 C. M. Phelps et al.: Microbiomes of Western Australian marine environments The term ecosystem engineer’ refers to an organism A central, but overlooked, component to that directly or indirectly modulates the availability of understanding drivers of seagrass decline is the role resources (other than themselves) to other species, of microbes living in association with their host as a by causing physical state changes in biotic or abiotic single biological unit also referred to as the 'holobiont' materials, in so doing they modify, maintain and/or create an (see pull-out box, below; Ugarelli et al., 2017). Seagrass ecosystem. tissues are colonised by a diverse microbiome that play a critical role in their growth and health due to their The seagrass meadows of Western Australia are influence on nitrogen and phosphorus supply (Garcias- among the most diverse in the world, with 11 genera Bonet et al., 2016, Tarquinio et al., 2018), protection from and 26 species of seagrass that represent 36% of global pathogens (Marhaeni et al., 2011, Supaphon et al., 2013), seagrass diversity (Short et al., 2007). Seagrasses in sediment detoxification (e.g., removal of sulphides; Western Australia are distributed along a latitudinal Kiisel et al., 2006) and production of phytohormones range, which stretches from 13°S to 35°S (Short et al., that stimulate plant growth (Kurtz et al., 2003). For 2007). These meadows cover an estimated 20 000 km2(ca example, cyanobacteria associated with seagrass leaves 43% of the total Australian seagrass area) and include and sulphate-reducing bacteria present in the roots may both temperate and tropical species (Kilminster et al., supply up to a third of the nitrogen requirement by 2015). Northern Western Australia is dominated by the seagrass through nitrogen fixation and/or mineralisation tropical species Thalassia hemprichii and Thalassodendron of organic nitrogen (Welsh, 2000; Nielsen et al., 2001; Cole ciliatum, which both have ranges that reach to 22°S, a & McGlathery, 2012). Seagrass epiphytic cyanobacteria latitude that also corresponds to the northerly limit of and fungi also represent a source of antimicrobial, the temperate seagrass Amphibolis antarctica (Walker, antifungal and antifouling molecules and can protect 1989; Kirkman, 1997). Cymodocea angustata, Halodule seagrasses from pathogens and biofouling (Gleason & uninervis, Halophila spinulosa and Syringodium isoetifolium Paulson, 1984; Supaphon et al., 2013; Mazard et al., 2016). reach south to Shark Bay at 26°S (Walker, 1991; Kirkman, 1997). Southern Western Australia is dominated by The term ‘holobiont’ refers to an assemblage of different Posidoniaceae with eight Posidonia species inhabiting interacting organisms considered as a single unit. For either exposed or protected areas according to the habitat example, a host organism (such as seagrasses, sponge, fish requirement of the species (Carruthers et al., 2007). Over etc.) and the microbes that live in and on that host, and their 1000 research papers and books have been published entire genetic repertoire. since the early 1980s on the ecology of Australian Microbial populations respond rapidly to seagrasses, with much of this research conducted along environmental disturbance due to their fast generation Western Australia (York et al., 2017). Within Western times (Allison & Martiny, 2008). Consequently, Australia, seagrasses play a central role in sustaining monitoring their composition and activity can serve as the aquaculture industry (Hanson et al., 2005; Ince et a sensitive bio-indicator of environmental fluctuations al., 2007; Blandon & Zu Ermgassen, 2014). For example, and ultimately declines in seagrass health. Despite seagrass meadows provide foraging grounds for the the globally recognised importance of microbiomes western rock lobster Panulirus cygnus, whose fishery is to seagrass health, research on their microbiomes valued at an estimated AUD $200 million (De Lestang is fundamentally lacking, particularly in regard to et al., 2009). Seagrass wrack is also an important habitat Australian taxa. A recently published overview of when it is deposited in surf zones where it sustains seagrass microbiome research revealed that only three various components of the coastal ecosystem by feeding of 58 studies worldwide were on Australian ecosystems amphipods, copepods, birds, crabs and a variety of (Ugarelli et al., 2017). While this review was not juvenile fish (Lenanton, 1982; Robertson & Lenanton, exhaustive, it serves to highlight the discrepancy between 1984; Hyndes & Lavery, 2005; Ince et al., 2007). the many studies on Australian seagrass and the small Despite the importance of seagrass meadows in portion that focus on the microbiome. Western Australia, there has been an extensive decline Whereas few research articles have been published in their area across the State, largely as a result of coastal on Western Australian seagrass microbiomes compared development and climate change (Hyndes et al., 2016). to other host-associated microbiomes (Fig. 2), this For example, in Cockburn Sound (Leeuwin-Naturaliste research has led to several important discoveries. Bioregion, Fig. 1), 97% of the seagrass meadow (34 km2) Research on temperate Posidonia sinuosa communities has had been lost by 1978 due to development of heavy revealed the importance of leaf-associated microbiota in industries and the consequent flow of industrial waste translocating nitrogen into seagrass leaves (Tarquinio and nutrients into the bay (Cambridge & McComb, et al., 2018). Ureolytic and ammonia-oxidising genes 1984). Similarly, at Albany up to 66% of the seagrasses in are significantly more abundant in the leaf microbiome Princess Royal Harbour and up to 46% of the seagrasses than in the surrounding habitat, indicating that there is a in Oyster Harbour (South Coast Bioregion; Fig. 1) have specific ecological niche for ammonia-oxidising bacteria declined due to elevated nutrient flow from local factories in a function traditionally considered to be dominated and town sewage (Bastyan, 1986; Kirkman, 1987). In 2011, by archaea (Tarquinio, 2017). This work suggests a a particularly strong marine heat wave event caused previously unrealised role of the leaf microbiome in damage to 36% of the seagrass meadow area in Shark Bay nitrogen cycling, likely of global significance considering (Arias-Ortiz et al., 2018). In most cases seagrasses have the abundance of seagrass habitats worldwide. failed to recover despite improvements in water quality (Mohring & Rule, 2013; Fraser et al., 2016). This has led Other seagrass microbiome research in Western to a greater research effort to identify possible reasons Australia focusses on identifying links between above for continued seagrass decline, as well as more focused ground disturbances to seagrasses and changes in the research effort into improving seagrass restoration. below ground microbial communities. For example, light 21 Journal of the Royal Society of Western Australia, 101, 2018 reduction at the leaves increased root exudation in three of the role and diversity of eukaryotic microorganisms Western Australian tropical seagrass species (Martin associated with seagrasses, together with their resilience et al., 2018), and led to a reduction in the abundance of to change, is essential (York et al., 2017). Priorities for beneficial bacteria within the root microbiome (Martin et future research should include focusing on sediment al., 2017). Fraser et al. (2016) quantified threshold organic detoxification and nutrient acquisition processes, as matter loads that cause shifts in microbial community well as those involved in pathogen defence (York et al., structure of the seagrass sediment microbiome. This 2017). Given recent marine heat waves along the Western threshold coincided with a reduction in sediment pH, Australian coast (Arias-Ortiz et al., 2018), understanding possibly favouring microbes such as sulphate reducers how increasing temperature affects seagrasses and their that require little or no oxygen. associated microbiomes should also be a priority (Hyndes et al., 2016) to improve our current knowledge of seagrass The spatial structure and colonisation pattern of die-off events and to help restorative efforts across microbes have been examined in several Western Western Australia. Australian seagrass species. For example, scanning electron microscopy revealed that colonisation of Coral Microbiome microbes on Posidonia australis roots was lower (2.5 x 105 cells/cm2) than on Mediterranean Posidonia species (P. Globally, shallow-water coral reef systems represent one sinuosa 4.89 xlO5 cells/cm2 and P. oceanica 4.43 x 106 cells/ of the most diverse, complex, productive and valuable ecosystems (Crossland et al., 1991; Moberg & Folke, cm2), possibly due to the older age of the Mediterranean 1999). Such reefs are mostly located in oligotrophic, intra- species roots compared with their Western Australian counterparts (Garcia-Martinez et al., 2005). Scanning tropical regions, where environmental characteristics (i.e. salinity and temperature) lie within the range necessary electron microscopy also revealed that microbial root to support the growth of reef organisms (Kleypas et colonisation of three tropical Shark Bay seagrasses was al., 1999). However, Western Australian shallow coral highest in the root hair zone compared to other parts of reefs also include fringing and atoll reefs found in the the root, possibly due to differences in root exudation and leakage of oxygen along the root length (Martin et transition zones between temperate and tropical waters al., 2018). Transmission electron microscopy and light where mean water temperature ranges between 20 to 24°C, several degrees cooler than the optimal coral microscopy also revealed fungal hyphae penetrating the root cells of Western Australian Posidonia spp. (Kuo et reef temperatures of 23 to 29°C. These environmental al., 1981) and the mesophyll shoot tissue of the seagrass features have generated diverse habitats with unique Zostera muelleri (Kuo et al., 1990), but little else is known coral communities along the coast. The Ningaloo Reef, approximately 260 km long, is the only extensive coral about fungi on seagrasses in the State. reef fringing the west coast of the continent (Ningaloo Seagrasses influence not only the microbes directly Bioregion, Fig. 1). Most other reefs in northern Western associated with their own root tissues, but they may Australia either suround offshore islands or are on also drive shifts in the bacterial communities within the emergent points along the continental shelf where immediate surrounding sediment (the rhizosphere), waters are clearer than inshore regions (e.g., Rowley which, like terrestrial plants, represents a hot spot of Shoals, Scott and Seringapatam Reefs, Pilbara Bioregion; microbial activity (Shieh & Yang, 1997). Rhizosphere Fig. 1). The most southerly reef-forming coral species microbes benefit from plant metabolism (e.g., delivery in Western Australia are found in the Abrolhos Islands of photosynthetically produced oxygen and dissolved Bioregion (Fig. 1). Those reefs lie within a region of organic carbon by roots), but they may also profoundly convergence between temperate and tropical waters, and influence seagrass fitness. For example, eutrophication are considered unique as corals coexist with temperate of coastal waters has been linked to major seagrass macroalgae communities. Coral species are also present die-off events due to the stimulation of nitrogen and as far south as the Leeuwin-Naturaliste Bioregion, phosphorus on decomposition and reduction processes i.e., Rottnest Island, Geographe Bay and Recherche of sulphate reducing bacteria; leading to an increase Archipelago, but have a patchy distribution in these in the accumulation of phytotoxic sediment sulphides regions and do not form extensive reef substrate (Veron (Bagarinao, 1992; Borum et al., 2005; Holmer et al., 2006). & Marsh, 1988). However, nutrient additions and elevated temperatures Shallow water corals are able to grow in otherwise were found to have negligible effects on the rate of oligotrophic waters due to their ability to establish decomposition of detritus from the seagrass Zostera mutualistic symbiotic relationships with unicellular muelleri under anoxic conditions, despite causing changes dinoflagellate algae of the Family Symbiodinaceae, in microbial community composition (Trevathan-Tackett as well as with bacteria and archaea. Corals also host et al., 2017). Further studies are needed to understand fungi and viruses, whose functional roles are not well the delicate equilibrium that regulates seagrass and understood (Rosenberg et al., 2007). Functionally, rhizosphere bacterial interactions. coral-associated symbionts are involved in nutritional Collectively, these studies represent the 'tip of the pathways, i.e. photosynthesis, nitrogen fixation, iceberg' with regards to understanding the importance phosphate production and solubilisation, degradation of of microbes in Western Australian seagrass ecosystems. dimethylsulfoniopropionate (DMSP); bacterial cell-cell It is clear that there are large gaps in our knowledge chemical signalling (also known as quorum sensing); of the microbial ecology of seagrass ecosystems from genetic exchange; and protection of the host (Muller- both a national and local context. As the global extent Parker & Delia, 1997; Rosenberg et al., 2007; Siboni et of seagrasses has been declining at an increasing rate al., 2008; Sharp & Ritchie, 2012; Fournier, 2013). For (Waycott et al., 2009), focused efforts on effective science- instance, through their ability to produce secondary based management, such as an improved understanding metabolites and nutrients (Lesser et al., 2007; Olson et 22 C. M. Phelps et ah: Microbiomes of Western Australian marine environments ah, 2009; Howard et ah, 2011; Raina et ah, 2013), bacteria Island (mean SST from 19 to 23°C). Interestingly, both belonging to specific lineages (i.e. Vibrio, Pseudomonas and studies found minimal variation in microbial community Cyanobacteria) are likely to contribute to the control of structure despite the large distance between sampling Symbiodinaceae's growth, density and nutrition (Ritchie sites and substantial differences in annual mean SST. & Smith, 1997; Lesser et ah, 2007). Conversely, the ability One possible mechanism for the similarity between of the Symbiodinaceae to produce DMSP potentially sampling regions may be the connectivity of Western controls nutrient availability and consequently the Australian reefs via oceanographic features (e.g., the growth of bacterial populations, some of which may be Leeuwin Current) that are likely to be the main pathways pathogenic (Curson et ah, 2011; Raina et ah, 2016; Raina et connecting Symbiodinaceae and bacterial communities ah, 2017). Preliminary studies suggest a role for archaea of the tropical north with the temperate south regions in the recycling of nitrogen within the coral host (Siboni of Western Australia. With regards to Symbiodinaceae et ah, 2008), whereas viruses may help in controlling communities in Western Australian Acropora corals, bacterial abundance in the coral mucus (Wood-Charlson Thomas et ah (2014) show that most colonies had a et ah, 2015). high level of specificity to clade C, as well as a novel association with clade G, in contrast to studies in other Most coral microbiome research across Australia regions where clade G has not been detected in Acropora. has been conducted on the iconic Great Barrier Reef, in A biogeographical study of bacteria and archaea north eastern Australia, with far fewer investigations on associated with the coral Stylophora pistillata from seven the west coast (Crabbe & Carlin, 2009; Ceh et ah, 2011; major regions across the globe also showed unique Ainsworth et ah, 2015; Thompson et ah, 2015a). However, features of the holobiont in corals from Western Australia there are several important examples of coral microbiome (Neave et ah, 2017): among these regions, only Western research from Western Australia. For instance, the Australian corals were found to host distinct lineages role of nitrogen transfer to coral larvae by two strains of the coral-associated Gammaproteobacterial genus of Gammaproteobacteria was investigated within the Endozoicomonas. S. pistillata from Western Australia also cosmopolitan coral species Pocillopora damicornis via contained high numbers of Pseudomonas, not seen in other nanoscale secondary ion mass spectrometry (Ceh et ah, regions. Although this comparison is based on just two 2013a). When larvae were exposed to either strain, there studies, taken together they suggest Western Australian was increased nitrogen uptake, providing evidence corals exhibit unique microbial assemblages, arguably for the role of microbes in nutrient transfer during this promoting the importance of Western Australian corals as critical early life history phase (Ceh et ah, 2013a). Two an endemic reservoir of microbial diversity. other examples have focused on microbial community structure during and after spawning. The first examined Despite their isolation. Western Australian coral Acropora tenuis, P. damicornis and Tubastrea faulkneri reefs are not immune to climatic events and other and detected an increase in Alphaproteobacteria human related impacts. Large-scale disturbances (such after spawning, with the Roseobacter clade found to the marine heatwave in 1998) have had relatively little be conspicuous in all three species after spawning, impact on Western Australian corals (Speed et ah, 2013). suggesting they may play a role in coral reproduction However, record temperatures of up to 5°C above long¬ (Ceh et ah, 2012). The second of these studies found term averages during 2010/11 caused major bleaching that A. tenuis (a broadcast spawning species), and P. (loss of Symbiodinaceae) and significant loss in coral damicornis (a brooding species) each released specific cover along parts of the Western Australian coast (Pearce microbial assemblages into the surrounding seawater et ah, 2011, Moore et ah, 2012, Depczynski et ah, 2013). during spawning (Ceh et ah, 2013b). In particular, Local impacts of sedimentation due to dredging is also A. tenuis released, in decreasing order, Roseobacter, an important environmental impact in Western Australia, Flavobacteriaceae, Alteromonas and Shewanella, again particularly in the Northwest Province Bioregion implying a role for some Roseobacter in the reproductive (Jones et ah, 2015). Increased sedimentation rates and processes of corals. In contrast, P. damicornis released turbidity caused by dredging and deposition of dredge Alteromonas, Vibrio, Shewanella and Marinomonas with only spoil can reduce light available to Symbiodinaceae minimal amounts of Roseobacter detected in the water for photosynthesis (Bessell-Browne et ah, 2017), with column post-spawning. These studies add to several potential consequences for other components of the others from different geographical locations (e.g., Apprill coral microbiome, and as a result coral health. For et ah, 2009 and Sharp & Ritchie, 2012) and indicate the example, altered coral holobionts have the potential to presence of Alphaproteobacteria, and in particular make corals more susceptible to disease and bleaching the Roseobacter clade, as key coral associates in either events (Hughes et ah, 2017), as well as reducing rates of spawning corals or early life-history stages. fertilisation, larval survival and settlement (Erftemeijer Several studies have examined geographic variation of et ah, 2012). However, the consequences of altered distinct components of the coral holobiont in contrasting environmental conditions on Western Australian coral regions within Western Australia. Given the extensive microbiomes are still poorly understood with regards to coastline. Western Australia presents opportunities to diversity, abundance and functionality, including their connection with coral health (Pollock et ah, 2014). examine microbiomes of coral species in vastly different environmental conditions. Thomas et ah (2014) examined Symbiodinaceae community variation within Acropora Temperate macroalgal microbiomes from the Kimberley region (mean SST from 26 to 31 °C) and the Abrolhos Islands (mean SST from 20 to 25°C), Temperate reefs, dominated by macroalgae, are whereas Ceh et ah (2011) examined coral-associated ecologically, culturally and economically important bacteria in the coral species Pocillopora damicornis at (Harley et ah, 2012). Macroalgae provide many essential Ningaloo Reef (mean SST from 22 to 28°C) and Rottnest roles in marine ecosystems (Steneck et ah, 2002), such as 23 Journal of the Royal Society of Western Australia, 101, 2018 primary production, the provision of habitat (see pull¬ of macroalgal biomass and habitat (Egan et al., 2014; out box, ecosystem engineers, page 21), nutrient retention/ Beattie et al., 2017). For example, Marzinelli et al. (2015) cycling, as well as C02 storage (Egan et al., 2013; Koch observed dysbiosis (see pull-out box below) of Ecklonia et al., 2013). Macroalgal growth, health, resilience and radiata microbiomes along the temperate Australian ecological function are all influenced by the interactions coastline (Marzinelli et al., 2015) and Ecklonia radiata with the associated microbiome (Case et al., 2011; Egan infected with a putatively pathogenic bacteria displayed et al., 2013). The relationship between microbes and bleaching (Beattie et al., 2017). These observations show macroalgae can be mutually beneficial, parasitic, or that the kelp microbiome is linked to both bleaching and commensalistic (Armstrong et al., 2001; Case et al., 2011; temperature and may play a direct role in decline of kelp Abby et al., 2014). For example, a study from the United health. Kingdom using the green alga Ulva linza, found that The term dysbiosis’ refers to a microbial community shift particular strains of bacteria positively influenced the that has a negative impact on the host. growth and morphology of seaweed, whereas algae without these bacterial isolates displayed abnormal Changes in environmental conditions such as sunlight, growth and morphology (Marshall et al., 2006). Fungi chlorophyll-a, water temperature and salinity impact also form beneficial associations with macroalgae and the community structure of macroalgae microbiomes obligate symbioses, termed mycophycobioses, and have (Gilbert et al., 2010). Future microbial studies should been described in brown, red and green macroalgae seek to understand the influence and interactions of (Raghukumar, 2017). Overall, microbial communities environmental, biological and anthropological factors are an integral component of sustaining normal algal on the Western Australian macroalgae holobiont. In function and are therefore important for the entire particular, rising seawater temperatures have been macroalgal ecosystem (Burke et al., 2011). flagged as a major contributor to diminishing macroalgal cover and range contraction of many macroalga species Western Australian benthic reef ecosystems, from along this coastline (Wernberg et al., 2011b, 2016b) the Northwest to the Southwest Province (Fig. 1), host suggesting that improved understanding of the influence diverse assemblages of macroalgae (e.g., Huisman, of rising water temperatures on macroalgal microbiomes 2018). An early study of macroalgal microbiomes is timely. Increasing urbanisation also has an impact examined aerobic heterotrophic bacteria containing on macroalgal microbiomes, with the kelp growing bacteriochlorophyll on various substrates, including on harbours and other marine structures displaying red and green species of macroalgae, and found high microbiomes similar to those found on diseased algae abundances on Western Australian algae (Shiba et al., (Marzinelli et al., 2018). Further research is needed to 1991). More recently, the microbiome of the brown kelp, understand the flexibility, resilience and ecological Ecklonia radiata, was found to be stable in composition significance of macroalgal microbiomes and their role in among healthy individuals across the entire southern reef health along the Western Australian coast. coast of Australia (Marzinelli et al., 2015). The two other studies of macroalgae microbiomes from Western Marine vertebrates Australia indicate important ecological roles, including being the main decomposers of beach wrack on Western A number of endangered marine mammals live, or Australian sandy beaches (McLachlan, 1985) and cues for migrate, along the west coast of Australia, including settlement of marine invertebrates (Huggett et al., 2018). blue and humpback whales, dugongs and sea lions. In addition. Western Australian coastal waters support There has been a substantial body of work on the six of the world's seven species of sea turtles as well microbial ecology of several macroalgal species from as recreational and commercially valuable finfish and eastern Australian temperate waters, including several aquaculture fisheries. The role of the microbiome in species also present in Western Australia. These include vertebrates has been extensively studied in terrestrial studies of the red alga, Delisea pulchra, and its role in systems, facilitated by the explosion of human preventing microbial biofilms forming on algal surfaces microbiome research in the last decade. Mutualistic (Maximilien et al., 1998; Rasmussen et al, 2000; Manefield relationships between microbes and vertebrate hosts et al., 2002), as well as the ability of bacteria from the have evolved through co-evolutionary processes over green alga Ulva lactuca to prevent biofouling (Holmstrom long periods (Backhed et al., 2005) and have been linked et al., 1996, Egan et al., 2000, Egan et al., 2001, Holmstrom to changes in host phylogeny (Colston & Jackson, et al., 2002). Given the different oceanographic 2016). Virtually all external surfaces including the skin, characteristics that influence the macroalgal communities gastrointestinal tract and respiratory tract of vertebrates of Australia's east and west coasts and the high levels are colonised by microbes (Montalban-Arques et al., macroalgal endemic species on the west coast, similar 2015). Within these microbial communities, selective studies on the western microbiomes are required. pressures exhibited by the host and microbial members In temperate Australian waters, including those in produce highly structured populations of microbiota the west, the brown kelp Ecklonia radiata is the dominant (Moeller & Ochman, 2014). Our understanding of the habitat-forming alga (Kirkman, 1981). In recent years, metabolic capabilities of the microbiome and its role in kelp distribution and biomass has declined on both host health has been mostly advanced through molecular the east and west coastlines mainly due to rising water studies involving humans and captive mammals (Colston temperature (Wernberg et al., 2011a) and associated & Jackson, 2016). However, there are over 17 000 marine bleaching (loss of algal photosynthetic pigment) in this vertebrate species (Appeltans et al., 2012) and most of species (Phelps et al., 2017). Some evidence suggests these have received little or no attention with regards to that microbes could play a substantial role in the decline microbiome research. 24 C. M. Phelps et ah: Microbiomes of Western Australian marine environments Despite the continual exposure of marine vertebrates Despite the requirement for long-term protection to seawater, species-specific communities of microbiota of sea turtles, the microbiome of Western Australian have been found on the external surfaces of marine fish populations, including the endemic flatback turtle, and (Larsen et ah, 2013, Lowrey et al., 2015), whales (Apprill the Indian Oceans largest population of hawksbill turtle, et ah, 2014, 2017), dolphins and sea lions (Bik et ah, 2016). have not been described (Pendoley et ah, 2016). Sea turtles Microbial communities are further structured according receive little to no maternal care, consuming seagrass to unique environments in different niches in and on from an early age and rely heavily on the hindgut vertebrate hosts, with the gastrointestinal (GI) tract the microbial fermentation for digestion. The gut microbiota most well studied region. Marine fish GI tracts have been is therefore strongly influenced by environmental and the most studied, especially for commercially important dietary factors which change as the turtles mature from species (Colston & Jackson, 2016). The first meal (first juvenile to adult (Price et ah, 2017). Building on this work, feeding) taken by a fish has a strong influence on the how the gut microbiome influences the development overall composition of the GI microbiome (Ingerslev et of marine hindgut fermenters, particularly in terms of ah, 2014), but the homeostatic composition is continually dietary requirements, would be relevant for rehabilitation modified by interconnecting factors including host and protection programs in Western Australia. genetics, environment (water, diet, toxins, antibiotics, Finally, aquaculture is an important economic pH, temperature), and microbial inhabitants (competitive development in Western Australia, with production inhibition, metabolic activity). If the community expected to continue increasing especially within the composition is altered, and key microbial members are Midwest Aquaculture development zone, declared in lost (see pull-out box, dysbiosis, page 24), host benefits 2017 (Western Australian fisheries) and the Central West such as metabolic functioning (Rios-Covian et ah, 2016), Coast Bioregion (Fig. 1). A number of tropical native pathogenic exclusion, and immune function (Maynard species are raised in aquaculture, and one of the greatest et ah, 2012) are impaired, and inflammation and disease challenges they face is bacterial disease, with most may progress (Montalban-Arques et ah, 2015). Infections bacterial species isolated from Australian aquaculture are common among marine mammals (Nelson et ah, environments (including those from Western Australia) 2015), and the role of the resident microbiota in the presenting antibiotic resistance (Akinbowale et ah, etiology of these conditions is poorly understood. 2006). Due to the broad target range of antibiotics, both Dysbiosis is a relatively new way of considering disease pathogenic and beneficial bacteria are affected, which can progression, and, as disease is one of the main causes of lead to dysbiosis, immune suppression and possibly an death in marine mammals (Waltzek et ah, 2012), it may increase in pathogen susceptibility (Becattini et ah, 2016). be an important focus for marine vertebrate microbiome As an alternative, probiotics and prebiotics are being research. investigated as an effective method for combating disease in aquatic animals (Banerjee & Ray, 2017). Probiotics have With the exception of sea lions, the microbiome been shown to deliver the same health benefits to the associated with marine mammals has not been studied host as a healthy microbiome (immune system, nutrition, within Western Australian populations. Healthy pathogen exclusion), although there have also been humpback whales from the North Atlantic, North reports that probiotics are not fully retained (Akhter et Pacific and South Pacific have a similar skin microbiome ah, 2015). The increasing demand for sustainable seafood dominated by specific bacteria (Tenacibaculum and and the growing Australian population means the health Psychrobacter) that is greatly reduced on entangled or management within aquaculture must be a top priority if deceased whales (Apprill et ah, 2014). On the east coast of disease-free fish production is to be maintained. Australia, faecal microbiomes from captive dugongs are less diverse than those of wild dugongs and are missing The high biodiversity and endemism of Western many bacterial members that dominate the wild dugong Australian marine organisms makes the coast an exciting microbiome (Eigeland et ah, 2012). Delport et ah, (2016) place to study marine vertebrate microbiomes and with found a similar result in wild and captive Australian the past warming anomalies in sea surface temperature, sea lions and presumed for both cases that contrasting the resulting range shifting species (Wernberg, 2012) diets between wild and captive animals played a key present a unique system in which biogeographic patterns role in the development of the different GI microbiomes. of the microbiome can be studied within a single species Furthermore, the captive dugongs were orphaned at in the wild. Both captive animals, and model systems one and three weeks, so it is possible they may not have (such as the Zebrafish) have been used to reveal the had sufficient suckling time to develop a 'normal' gut functional role of the microbiome, improving our microbiome (Eigeland et ah, 2012). It would be valuable understanding of co-evolutionary mechanisms that to do comparable studies, examining differences between influence community structure. However, to understand west coast wild and captive vertebrates as well as how the host-symbiont relationship responds to changes their east coast counterparts to further understand the in the natural environment, the resilience and metabolic structure of Western Australian vertebrate microbiomess. flexibility of bacterial members should be studied within In particular, respiratory microbiomes are likely to be a a single host species, eliminating variation caused by useful target as the respiratory tract is one of the most capture, or interspecies differences. When a host moves commonly affected sites in cetaceans (Apprill et ah, 2017), into a new environment, key questions arise such as: will and oil exposure is known to cause respiratory problems the microbiome be restructured by the new metabolites (Thomas et ah, 2016). Conducting similar research on and populated by new seeding bacteria, or can the same humpback whales and bottlenose dolphins along the species persist by changing their metabolic output? Such North West Shelf—an extensive oil and gas region—may questions can be addressed by targeting range shifting be of particular importance. species along the Western Australian coast such as Choerodon rubescens (Cure, 2018), and Chaetodon assarius 25 Journal of the Royal Society of Western Australia, 101, 2018 (Wernberg, 2012), and comparing the microbiome from cyanobacteria in the Kimberly region and a recent study distinct populations over large distances. Furthermore, from Rottnest Island in southwestern Australia found researchers could track the movement of potential similar amounts of the two cyanobacterial groups, and pathogens from historic to new populations, which could about one order of magnitude fewer picoeukaryotes improve conservation efforts as well as improve our (Thomson & Pattiaratchi, 2018). The study reports understanding of the relationship between dysbiosis and little seasonality in picophytoplankton abundance, disease in marine vertebrates. and suggests that their abundance increases following marine heat waves. These microbes are good markers Plankton microbiome of long-term tropicalization as Prochlorococcus prefers warmer temperatures and less nutrients (Li, 2009). Seawater is amongst the most abundant compounds They also indicate oceanographic features, such as the on the Earth's surface, covering more than 70% of the warm-core eddy linking Leeuwin Current, shelf and planet. One millilitre contains approximately 10 million oceanic waters, observed off southwestern Australia by viruses, 1 million prokaryotic cells and 1000 unicellular Paterson et al. (2013). A study of their relative abundances eukaryotes (e.g., Kirchman, 2008). In addition to their between El Nino and La Nina periods (July 2009 - June enormous biomass, planktonic microorganisms also 2010 vs La Nina of July 2010 - June 2011) showed harbour extensive genetic diversity, and thus drive global increased abundances of cyanobacteria, and particularly biogeochemical transformations including the nitrogen of Prochlorococcus in the Rottnest Island and Esperance and carbon cycles (Falkowski et al., 1998). While recent regions, indicating a general tropicalization of the waters 'omics technologies and global ocean surveys (e.g., (Thompson et al., 2015b). Sunagawa et al., 2015 and Yooseph et al., 2007) have greatly facilitated our knowledge of global oceanographic Despite the abundance, activity, diversity and trophic patterns and processes, understanding key drivers of role of the heterotrophic prokaryotes as essential oceanic microbial community diversity and function components of the microbial food web affecting the ocean remain a global challenge. In spite of that, we know very carbon cycle (Whitman et al., 1998), we know little of their little of which microbes dominate in Western Australian role in the marine waters of Western Australia. Patten et marine waters, in what abundances, what are the drivers al. (2011) enumerated bacterioplankton, virioplankton of planktonic microorganism abundance, activity or and picoautotrophs across the Ningaloo Reef and into the diversity, and how global change is affecting them. sandy lagoon and also measured active depletion through Within Western Australian waters, phytoplankton, the coral reef of all groups. They found that Synechococcus the microbes at the base of the food chain, were first to removal was biogeochemically more relevant, in terms be investigated among the planktonic marine microbes, of C and N, and that viruses were less affected by the possibly because measures of chlorophyll-a concentration, coral than the other microbial groups. Jones et al. (2014) an indicator of phytoplankton biomass, were an easy way compared the abundances of bacteria, picophytoplankton of characterising the trophic conditions of an aquatic and viruses across a macrotidal complex archipelago in environment. Conspicuous eukaryotic phytoplankton Collier Bay, north of Broome. They observed a mosaic were the first studied microbes (e.g., Hallegraeff & Jeffrey, of concentrations with abundances typical of a tropical 1984), and monographs exist about diatoms (Jameson site (1 x 104 Synechococcus, 3 x 105 bacteria, 1 x 106 & Hallegraeff, 2010; McCarthy, 2013a), dinoflagellates viruses, with a larger variability in viruses), with lower (McCarthy, 2013b) and coccolithorids (Hallegraeff, 1984), abundances near the coast where waters were more as well as the phytoplankton of Western Australian turbid. estuaries (John, 1983). Recent syntheses of phytoplankton In terms of diversity, Raes et al. (2014) used a abundance and biomass (Davies et al., 2016) and fingerprinting approach to study bacterioplankton chlorophyll-fl measurements (Davies et al., 2018) around community composition across a large latitude gradient Australia have been published, and the data made (10°S to 32°S) following the continental shelf break from public through the Australian Ocean Data Network Fremantle to Darwin in a study of nitrogen fixation. system (http://portal.aodn.org.au/). Comparison of The authors found that bacterial communities were phytoplankton communities in the east (affected by the unique among the different water masses that are well Eastern Australian Current) and the west (affected by the defined by oceanographic parameters. In a subsequent Leeuwin Current) showed an overall difference in total study Raes et al. (2018), used tag sequencing to show a chlorophyll (0.14 to 0.25 pg Chi a H in the west, about powerful diversity gradient between the northernmost half the annually integrated value in the east (Thompson area, characterised by high temperatures and low et al., 2011). The Southwest coast has also been shown to diversity, and the lowermost area, characterised by have relatively few smaller eukaryotes (pelagophytes, lower temperatures and higher diversity. Bacterial prasinophytes, cryptophytes, chlorophytes) and fewer richness almost doubled between the two areas, and was larger eukaryotes (bacillariophytes and dinophytes) positively correlated to total dissolved inorganic nitrogen, reflecting the differences in seasonality of the two major chlorophyll-fl, phytoplankton community structure, boundary currents, the vertical stability of the water and primary productivity. Further analysis of these data column, and the average availability of nutrients in the (Raes et al., 2018) showed that the differences in bacterial euphotic zone (Blondeau-Patissier et al., 2011). diversity existed even though most communities were In particular, there are few records of dominated by the same groups (SAR11, Synechococcus, picophytoplankton (cyanobacteria of the genera Flavobacteriaceae, Rhodobacteraceae, etc.) in similar Prochlorococcus and Synechococcus, as well as small proportions. The communities could be differentiated eukaryotes) in Western Australia. Thompson & Bonham into three groups, according to whether they originated (2011) observed a significant contribution of the two in the Timor Sea, the subtropical waters, or the Leeuwin 26