1 
 
Perspectives Paper: 1 
A horizon scan of priorities for coastal marine microbiome research 2 
  3 
Stacey M. Trevathan-Tackett1*, Craig Sherman1, Megan J. Huggett2,3, Alexandra H. 4 
Campbell4,5, Bonnie Laverock6, Valentina Hurtado-McCormick7, Justin Seymour7, Alana 5 
Firl8, Lauren Messer9, Tracy Ainsworth4,10, Karita L. Negandhi11, Daniele Daffonchio12, 6 
Suhelen Egan4, Aschwin H. Engelen13, Marco Fusi12,14, Torsten Thomas4, Laura Vann8, 7 
Alejandra Hernandez-Agreda10,15, Han Ming Gan1, Ezequiel M. Marzinelli4,16,17, Peter D. 8 
Steinberg4,16,17, Leo Hardtke7, Peter I. Macreadie1 9 
 10 
1 Deakin University, Geelong, Centre for Integrative Ecology, School of Life and 11 
Environmental Sciences, Burwood and Waurn Ponds Campuses, VIC, 3130 Australia  12 
2Centre for Marine Ecosystems Research and Centre for Ecosystem Management, School of 13 
Science, 270 Joondalup Dr, Edith Cowan University, Joondalup 6027 WA Australia  14 
3School of Environmental and Life Sciences, The University of Newcastle, 10 Chittaway Rd, 15 
Ourimbah 2258 NSW Australia  16 
4Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, 17 
University of New South Wales, Sydney NSW 2052, Australia 18 
5Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, 19 
QLD 4556, Australia 20 
6School of Science, Auckland University of Technology, Private Bag 92006, Auckland, New 21 
Zealand 22 
7Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, NSW 23 
2007, Australia 24 
8Genome Center, University of California, Davis, California 95616  25 
2 
 
9Australian Centre for Ecogenomics, University of Queensland, St Lucia, Brisbane, QLD, 26 
4072, Australia  27 
10Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook 28 
University, Townsville, QLD, 4811, Australia 29 
11Department of earth and planetary sciences, Macquarie University, North Ryde, NSW 30 
2109, Australia 31 
12King Abdullah University of Science and Technology (KAUST), Red Sea Research Center 32 
(RSRC), Thuwal 23955-6900, Saudi Arabia 33 
13Centre for Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 34 
8005-139 Faro, Portugal 35 
14School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK 36 
15The College of Public Health, Medical and Veterinary Sciences, James Cook University, 37 
Townsville, QLD, 4811, Australia 38 
16Sydney Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW 2088, Australia 39 
17Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological 40 
University, Singapore 637551 41 
 42 
*Corresponding Author. E-mail: s.trevathantackett@deakin.edu.au 43 
  44 
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Abstract 45 
Research into the microbiomes of natural environments is changing the way ecologists and 46 
evolutionary biologists view the importance of microbes in ecosystem function. This is 47 
particularly relevant in ocean environments, where microbes constitute the majority of 48 
biomass and control most of the major biogeochemical cycles, including those that regulate 49 
the Earth's climate. Coastal marine environments provide goods and services that are 50 
imperative to human survival and well-being (e.g. fisheries, water purification), and emerging 51 
evidence indicates that these ecosystem services often depend on complex relationships 52 
between communities of microorganisms (the ‘microbiome’) and their hosts or environment 53 
– termed the ‘holobiont’. Understanding of coastal ecosystem function must therefore be 54 
framed under the holobiont concept, whereby macroorganisms and their associated 55 
microbiomes are considered as a synergistic ecological unit. Here we evaluated the current 56 
state of knowledge on coastal marine microbiome research and identified key questions 57 
within this growing research area. Although the list of questions is broad and ambitious, 58 
progress in the field is increasing exponentially, and the emergence of large, international 59 
collaborative networks and well-executed manipulative experiments are rapidly advancing 60 
the field of coastal marine microbiome research. 61 
 62 
 63 
Keywords: bioremediation, core microbiome, dysbiosis, functional diversity, environmental 64 
stress, evolution, holobiont, microbial ecology 65 
 66 
___________________________________________________________________________ 67 
 68 
 69 
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Background 70 
Coastal marine ecosystems provide a range of ecologically and economically important 71 
ecosystem services, including habitat provisions, nutrient cycling, coastal protection and 72 
fisheries enhancement1. The health and services of these ecosystems are inherently linked to 73 
the microorganisms residing in these ecosystems (e.g. pollution remediation, disease and drug 74 
discovery2-4). As we increase our understanding of the importance of coastal marine 75 
microorganisms and their genetic makeup (i.e. the microbiome, see Box 1), the number of 76 
research articles describing the distribution, structure, and function of microbiomes 77 
associated with coastal marine ecosystems has flourished (Supplementary Figs. 1 and 2). The 78 
ecosystem services are largely attributed to the habitat-forming organisms, such as corals, 79 
sponges, macroalgae, seagrasses, mangroves and saltmarshes, which form the foundation of 80 
these ecosystems. Furthermore, due to the reliance of coastal marine ecosystem health on 81 
these habitat-forming organisms, the field has realized the importance of understanding the 82 
macroorganisms and their microbiomes as a synergistic ecological unit (i.e. holobiont, see 83 
Box 1). As a result, there has been a relative surge in host-associated microbiome research in 84 
recent years (Supplementary Fig. 1) aimed at identifying how microbiomes influence host 85 
phenotype, physiology, and development5-7. Although our understanding of several 86 
fundamental concepts in coastal marine microbial ecology has increased7,8, coastal 87 
microbiome research -- particularly in the context of holobionts -- is still in its infancy, 88 
especially relative to other microbiome fields, such as the human microbiome. A large 89 
number of open questions currently limits our capacity to assess how microbial processes 90 
influence the ecology of these environments, both under contemporary conditions and under 91 
future environmental change. Therefore, there is a clear need to prioritize and define key 92 
questions for future research that will allow for better assessments of how microbial 93 
processes truly influence the ecology and health of coastal marine environments. 94 
5 
 
 95 
[suggested Box 1 placement] 96 
 97 
Evaluating the state of the science 98 
To evaluate the current state of coastal marine microbiome research, we surveyed the current 99 
literature, then ‘horizon scanned’ with experts in the field to identify major research gaps, in 100 
order to determine where future challenges lie and ultimately progress this field of research 101 
(see Box 2 for description of the approach and limitations). For the literature search, we 102 
focused on six key holobionts that form the foundation of these coastal ecosystems - corals, 103 
sponges, macroalgae, seagrasses, mangroves and saltmarshes. We also considered the 104 
microbiomes of sediments and the water column within coastal marine ecosystems. The key 105 
findings from the literature survey include identification of areas of progress, as well as 106 
holobiont systems that need more attention (Supplementary Figs. 1 and 2). For example, 107 
research on seawater- and sediment-associated microbiomes has dominated coastal marine 108 
microbiome literature to-date (consistently ≥ 50% of the total number of studies), while host-109 
associated microbiome research is steadily increasing and has generally focused on coral and 110 
sponge holobionts (Supplementary Fig. 1). In the last five years, however, the diversity and 111 
quantity of microbiome and holobiont research has incrementally increased with the inclusion 112 
of macrophyte-associated microbiome studies, although mangrove- and saltmarsh-associated 113 
microbiome research is still nascent (Supplementary Fig. 1). Additionally, the methodologies 114 
used to describe coastal marine microbiomes has diversified over time from predominantly 115 
microscopy, cell counts, and community fingerprinting techniques, to sequencing-dominated 116 
technologies (Supplementary Fig. 1). The literature survey also identified geographic 117 
hotspots and gaps in microbiome studies (Supplementary Fig. 2). The coastlines of Australia, 118 
Europe, the northern Mediterranean Sea, the Red Sea and US are relatively well-sampled in 119 
6 
 
multiple ecosystem types, while there are clear regional gaps for host-associated microbiome 120 
studies along the South American, African and northern Asian coastlines. Some of the well-121 
studied regions are dominated by studies on specific host-associated microbiomes 122 
(Supplementary Fig. 2). For instance, seagrasses have been heavily studied in the temperate 123 
US, while the biodiversity hotspots in the Indo-Pacific have been dominated by studies on 124 
coral- and sponge-associated microbiomes (Supplementary Fig. 2).  125 
 126 
The horizon scan resulted in 108 questions key to progressing coastal marine microbiome 127 
research. Nearly half of the questions (~50) directly or indirectly concerned host-associated 128 
microbiomes, with the remaining covering a range of fundamental microbiome ecology or 129 
methodological topics independent of a specific ecosystem, host or substrate. In assessing the 130 
literature and identifying priority research questions via the horizon scanning exercise (see 131 
Box 2 for the methodology used), we outline seven microbiome research themes relevant to 132 
deciphering the role of microbiomes within coastal marine ecosystems. The themes begin 133 
with microbiome questions, followed by host-microbiome themes, and lastly questions 134 
concerning microbiomes and holobionts in the environment (Box Diagram 1). While some of 135 
the themes are holobiont-centric, we do not focus on one particular holobiont system. Rather 136 
the themes represent general concepts that can be applied to multiple substrate- or host-137 
associated, or free-living microbiome systems. Therefore, we have provided a diversity of 138 
references to support the presented themes throughout, with the aim to create a 139 
comprehensive vision that may unify the strategy of research on coastal marine microbiomes.140 
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 141 
[suggested Box 2 placement] 142 
 143 
Key research themes in coastal marine microbiome research 144 
 145 
Microbiome 146 
   147 
Theme 1: How can community structure be matched to microbiome function? 148 
In coastal marine ecosystems, enormous microbial diversity has been revealed via, for 149 
instance, phylogenetic analyses of the 16S rRNA gene (e.g. 8-10). However, it is important to 150 
define the function of a microbiome in order to understand how it is likely to influence its 151 
host and the ecosystem11.  Currently, the best way to directly determine the function of the 152 
entire microbiome is via metagenomic and metatranscriptomic sequencing12-16. The recent 153 
availability of many genome reconstruction or binning approaches17 offers a greater capacity 154 
to obtain near-whole genomes out of metagenomes, allowing a better understanding of the 155 
function of the microbiome members. However, our ability to successfully annotate 156 
functional genes within metagenomic and metatranscriptomic datasets remains outstripped by 157 
the availability of sequencing data itself. For example, extensive sequencing of the global 158 
ocean microbiome found that 40% of core orthologous genes were of unknown function18.  159 
 160 
Another approach to link diversity with function is to identify the ‘core microbiome’, or the 161 
persistent and functionally essential members of host-associated microbiomes, possibly a key 162 
determinant of host well-being and therefore overall ecosystem functioning and health (Fig. 163 
1)8,19. For example, conserved bacterial taxonomic groups, which constitute the coral core 164 
microbiome, play a critical role in the success of the coral-zooxanthellae symbiosis19. Other 165 
8 
 
organisms, such as the green seaweed Ulva mutabilis, require a core set of functions from 166 
their microbiome, rather than the presence of specific taxa20.  167 
Connecting diversity with function drives central ecological questions such as: (1) How does 168 
microbial community diversity influence functional aspects (e.g. resilience) of the host, 169 
microbiome and environment; and (2) How can we define the function of a coastal 170 
microbiome? Yet despite substantial effort in recovering metagenomes and 171 
metatranscriptomes from dominant marine hosts, there remain significant challenges in 172 
demonstrating causation between shifts in the microbiome and shifts in host health due to 173 
reduced capabilities to manipulate microbiomes in the field18 (e.g. manipulative field 174 
experiments, see Box 3). We recognize this as a particular challenge for microbial ecologists. 175 
Therefore, we identify several questions that we hope will move the field forward and lead 176 
into innovative approaches that determine the functional roles of coastal marine microbiomes, 177 
and thereby resolve the relationship between microbiome diversity and their functions: 178 
● How can novel techniques, e.g. single cell raman spectroscopy21, be applied to 179 
complex microbiomes and holobionts to interrogate microbial functions in situ? 180 
● How can intensive efforts for isolating coastal and host-associated microbes (i.e. 181 
‘culturomics’22) open the door for tracking the function of candidate genes and 182 
investigating homology, predictability and certainty of curated gene function? 183 
● How does identifying the core microbiome (taxa or set of functions, e.g. depicted in 184 
Fig. 1b-c, respectively) offer valuable insights towards advancing in-depth 185 
identification and experimental manipulation? 186 
 187 
[suggested placement for Figure 1] 188 
 189 
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Theme 2: At which spatial and temporal scales do the microbiomes of coastal organisms 190 
change? 191 
 192 
Host-associated microbiomes are highly dynamic communities that change at both small (i.e. 193 
ecological and physiological) and large (i.e. evolutionary and geographical) timescales. 194 
Substantial variability on very small spatial scales (i.e. within host) can be driven by host 195 
provisions, such as nutrient and oxygen availability10,23, as well as by trophic- and quorum 196 
sensing-related interactions among members of the microbiomes within a physical niche (e.g. 197 
24,25). Hosts also differ in microbiome community structure depending upon host distribution 198 
in a population (e.g. center vs. edge of a seagrass meadow26), and microbiomes on host 199 
species can also vary across large environmental gradients27. However, for some holobionts 200 
such as seaweeds, geographical variability in surface-associated microbiomes is relatively 201 
low even at continental scales, relative to other factors such as host health condition9. Short-202 
term temporal variability can also be surprisingly consistent, with predictable successional 203 
patterns over periods of days to weeks occurring in the epiphytic bacterial communities of 204 
macroalgae28, corals29 and sponges30. However, evidence for the scales at which coastal 205 
marine microbiomes shift in time and space, and the apparent drivers behind these shifts, is 206 
often conflicting. Studies showing host-specificity and stability in the microbiome over time 207 
and location10,28,31,32 contradict studies that suggest that microbial communities are highly 208 
dependent on the host physiological or environmental conditions9,33,34. These conflicting 209 
patterns prevent us from making generalizations about the stability or variability of coastal 210 
host-associated microbial communities (e.g. Theme 5). 211 
 212 
At evolutionary time scales, there is little doubt that hosts and their associated microbiomes 213 
influence each others’ evolution, and indeed at very large time scales, these interactions are 214 
10 
 
the basis for fundamental macroevolutionary events35. For individual marine systems, 215 
however, the details of how hosts and their microbial associates affect each other on shorter 216 
evolutionary time scales is limited, and whether or not these effects are broadly reciprocal 217 
(i.e. coevolutionary).  To date, there is limited evidence among benthic marine hosts for 218 
coevolution with their microbiome34,36, both because of the multiple interplaying factors that 219 
ultimately influence evolutive patterns, and because of the challenges in demonstrating 220 
formal coevolutionary relationships37. In some instances broad taxa of marine hosts and their 221 
microbiota appear to reciprocally evolve in response to one another38, but in others selective 222 
effects appear to be limited to the host and individual members of its microbiome rather than 223 
the entire microbial community39. Further complexities in teasing out the evolution of 224 
members in a holobiont include both internal microenvironments of the host that act like 225 
discrete coevolving ecosystems40, as well as the disparate evolutionary timescales that 226 
influence the host and the diversity of the microbiome members41. Evolutionary patterns 227 
within holobiont spatial niches/compartments have been shown for Scleractinian corals and 228 
their microbiomes, whereby the ecological relatedness of host-associated microbial 229 
communities parallels the phylogeny of related host species, and therefore evolutionary 230 
changes in the host associate with ecological changes in the microbiota42. This 231 
coevolutionary pattern, or phylosymbiosis was strongest in the coral skeleton compared to the 232 
coral tissue and mucus43. Although many coral-associated bacteria were host-specific, only a 233 
select minority of coral-associated bacterial families showed co-phylogenetic signals 234 
consistent with long-term host-microbe co-diversification43.  235 
 236 
Here, we outline key questions to progress our understanding of the scales at which 237 
microbiomes shift: 238 
 239 
11 
 
● What are the implications of disparate evolutionary timescales between the host and 240 
its microbiota? 241 
● How does the resolution at which we study microbiomes influence how we interpret 242 
differences in their composition and function at spatial and temporal scales? 243 
● Do the holobiont members differentiate between beneficial and detrimental 244 
relationships in order to selectively favor the transmission of mutualistic partners 245 
between generations, and if so, what are the mechanisms? 246 
 247 
To improve our understanding of the temporal and spatial dynamics of host-associated 248 
microbiomes, a structured approach to characterize spatial and temporal variation at multiple 249 
scales for both taxonomic and functional characteristics is needed. Future research should 250 
focus not only on descriptive studies, but also on perturbation experiments to assess resilience 251 
and stability under the context of variable systems44-46. Investigating microbiome evolution is 252 
inherently challenging, therefore clearly defining the boundaries of the question (e.g. 253 
phylogenetic vs functional level or the whole microbiome vs individual members), as well as 254 
identifying the limitations of what can be tested is necessary. Additional reflection on 255 
(co)evolution in systems other than coastal marine ecosystems may provide insight that could 256 
progress these questions. Examples include the formation of niches by symbiotic microbiota40 257 
and the broader literature on geographic aspects of coevolution (e.g. 47). 258 
 259 
 260 
Microbiome and Host 261 
 262 
Theme 3: How are host-microbiome interactions formed? 263 
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Several studies have established that most benthic organisms, including seagrasses10, corals31 264 
and macroalgae48, carry microbiomes that are distinct from the surrounding sediment or 265 
seawater. Yet, the timing and underlying mechanisms of microbiome acquisition (either host-266 
directed selection, or microbe-direct colonization) remain largely unresolved. Chemical 267 
signaling, specifically secondary metabolites produced by host species independently or in 268 
response to environmental or microbial cues, or signaling from microbial taxa that have 269 
already colonized the host, have been suggested to be important factors in both host defense 270 
against pathogenic microbes and microbiome colonization. For example, the pathogen Vibrio 271 
coralliilyticus has been shown to be attracted to corals that increase their production of the 272 
sulfur compound dimethylsulfoniopropionate (DMSP) under heat stress49. Conversely, in 273 
seaweeds such as Lobophora variegata, secondary metabolite production acts as a defense 274 
strategy by preventing colonization of pathogenic microbes, such as saprophytic marine 275 
fungi50.  276 
 277 
In addition to host-microbe interactions, some studies have suggested a role for microbe-278 
microbe interactions in determining microbiome composition, including lottery models51 and 279 
symbiotic modes of interaction31. It has also been shown that microbiome composition is 280 
affected by host condition (e.g. seaweed9; corals49), as well as environmental conditions (see 281 
Theme 5). Although there are few global census studies of the microbiome of particular 282 
marine species, recent studies in seagrasses10,33 suggest that microbial functions and 283 
microbiome composition are also affected by geographic location, indicating an influential 284 
role of the environment in shaping microbiome composition. Taken together, we hypothesize 285 
that the active role of the host in determining microbiome composition lies along a 286 
continuum, ranging from being determined by host condition to being determined by 287 
environmental factors, which no doubt affect host condition. Where the system lies within the 288 
13 
 
continuum is largely determined by host species. Additional studies in coastal marine 289 
ecosystems are needed to elucidate further: 290 
● What are the differing selection strategies between host species that determines 291 
whether the microbiome is shaped more by the environment or by the host? 292 
● What are the chemical pathways or specific processes by which a host attracts specific 293 
microbes, e.g. as observed in the model organism Arabidopsis microbiome52? 294 
● Does the host species dynamically change its selection strategies as a function of 295 
microbial colonization, or changing environmental conditions? 296 
 297 
To address these questions, controlled experiments in mesocosm systems are needed for the 298 
use of model organisms and standardized initial conditions. Tuneable manipulation of 299 
environmental parameters, addition of other microbial species, comparing a variety of host 300 
genotypes, and characterizing host exudate composition, could elucidate mechanistic 301 
interactions between host and microbiome, and discern the conditions under which a 302 
mechanism can be expected to occur. Some studies have made use of mesocosm 303 
systems44,53,54, and we expect even further advances from the use of controlled systems. 304 
  305 
 306 
Theme 4: To what extent is the resilience and health of the holobiont determined by the 307 
structure and function of its microbiota? 308 
The importance of microbes to the health of plants and animals is now well accepted. The 309 
microbial components of the holobiont can aid in digestion, provide essential vitamins and 310 
nutrients, protect from invading pathogenic organisms and stimulate developmental 311 
processes7,55,56. Therefore, any disturbance to the host microbiome are likely to result in a 312 
14 
 
breakdown of holobiont function (or dysbiosis), which can manifest itself as disease. 313 
Analogous disease concepts have been proposed for chronic conditions in humans, including 314 
common periodontal and gastrointestinal disorders, which are thought to result from a 315 
disturbance to the natural microbiota rather than infection by a singular pathogen57,58. While 316 
less well understood for marine holobionts, microbial dysbiosis may also play a role in 317 
diseases, for example, the bleaching diseases of invertebrates and seaweeds (e.g. see recent 318 
reviews59,60). However, with some exceptions61, the majority of these observations are based 319 
on correlative data, and the extent to which disease is a direct result of microbial dysbiosis 320 
remains an important research question. To fully appreciate the role of microbial dysbiosis 321 
we need to understand the core components of a healthy microbiome and identify those 322 
beneficial consortia that offer holobiont resilience. Importantly, given the capacity of 323 
microbes to rapidly respond, adapt and evolve to environmental conditions, the host 324 
microbiome is also likely to be instrumental in assisting the adaptation of higher organisms to 325 
future climate conditions or other anthropogenic stressors62. 326 
 327 
Structure and function of the microbiota within a holobiont can have important links to 328 
broader scale holobiont health and resilience. These connections are likely to aid in 329 
identifying core microbiome members and their corresponding functions essential for 330 
holobiont health (i.e. Theme 1). As we move to a changing climate, several key questions 331 
remain: 332 
● How do the interactions among microbiomes, within or across different niches of the 333 
same host affect host, resilience and homeostasis? 334 
● What are the criteria to designate specific taxa as beneficial core microbiome 335 
members or sentinels of dysbiosis in marine organisms? 336 
15 
 
● To what degree are members of the transient microbiome a source of functional 337 
redundancy and thus providing resilience during environmental change? 338 
 339 
Looking to the future, having sound knowledge and access to culturable, beneficial members 340 
of the core microbiota will have applied uses; for example, as biomarkers for the early 341 
detection of host stress or for the development of probiotic consortia that can be used to 342 
support aquaculture and marine restoration programs (Theme 6). However, taxa not 343 
considered part of the core microbiome under current conditions may become more important 344 
(core) under future conditions. 345 
 346 
 347 
 348 
Microbiome, Holobiont & the Environment 349 
 350 
Theme 5:  What is the role of the tripartite interaction, host-microbiome-environment, on 351 
holobiont resilience? 352 
 353 
Holobionts living in the dynamic ocean-land interface of coastal ecosystems63 can be exposed 354 
to substantial diel changes in temperature, salinity, tidal levels, light, oxygen, and nutrients64. 355 
Their resilience and adaptation is at least partially influenced by the microbiomes that 356 
modulate the environmental conditions to which they are exposed65. The environment can act 357 
as a source for holobiont microbiota that in turn are shaped by strong selective forces driven 358 
by the host biology and behaviours. For example, fiddler crabs carapace and gut66 are 359 
colonized by different pools of microbial colonists that are taken up from the environment, 360 
16 
 
but the burrowing and filter feeding behaviors of the crabs finely select such colonists from 361 
the sediment after strongly reconditioning its geochemical properties67. 362 
 363 
The effects of either short- or long-term environmental changes on host-microbiome 364 
interactions are inherently complex and thus difficult to predict68. The intrinsic environmental 365 
variability, for instance linked to seasonal changes69, perturbation events70, or a combination 366 
of these71, strongly influence microbiome diversity and functionality. Environmental stressors 367 
that can interact in opposing, additive or synergistic ways to influence hosts, microbiomes 368 
and their interactions, can lead to positive, negative or neutral impacts on them72. 369 
 370 
Using as an example thermal stress, frequently investigated in coastal marine microbiome 371 
research, we should consider that all organisms, whether microbial or macroscopic, have 372 
optimal thermal tolerance thresholds73. Thermal stress has been correlated with functional 373 
and/or structural shifts in microbiomes of corals74, sponges75 and oysters76, among others. 374 
Higher temperatures can induce virulence in otherwise commensal microbes77, and/or 375 
decrease the host chemical defences, with continued stress leading to the break-down of 376 
symbioses, the introduction of new microbes (e.g. opportunistic pathogens) and, eventually, 377 
deterioration of the host61,75. 378 
 379 
The ecological interactions within and among holobionts can also be indirect, for instance, 380 
microbiome recruitment by one host that may be affected by the exudates of another nearby 381 
host23,78. Host proximity may affect microbiome compositions, such as for algal turfs on the 382 
surface of Porites coral that were associated with increased alpha diversity of coral surface 383 
microbes, particularly of pathogenic bacterial taxa79. Host coexistence may also provide a 384 
more suitable habitat, e.g. seagrasses in anoxic sediments are favored by the aerobic sulfide-385 
17 
 
oxidizing bacterial symbionts associated with benthic burrowing bivalves, which detoxify the 386 
anoxic sediment80. 387 
 388 
Such tripartite interactions are highly complex and challenging to investigate in ‘real-world’ 389 
scenarios. We envisage the following research questions as priorities for the future research 390 
on coastal marine microbiomes: 391 
 392 
● How do environmental changes and stressors shape the functional redundancy of 393 
coastal microbiomes? 394 
● What are the environmental factors that determine and select microbiome members as 395 
beneficial or harmful for a host? 396 
● What are the chemical signals and how do they modulate the ecological interactions 397 
of microbiomes within and between holobionts and microbiomes? 398 
 399 
Investigations using real-world scenarios like those on combined multi-stressors, such as 400 
heat, pH (ocean acidification), and oxygen availability, are still rare68,81. However, in order to 401 
address the above question, such approaches are essential to build more ecologically reliable 402 
models on how host-microbiome interactions respond and adapt to changes82. Additionally, 403 
the holobiont approach sets a research framework, to comprehensively explore the adaptive 404 
and evolutionary patterns of organismal resilience and ecological function, in response to the 405 
critical challenges imposed by multiple combined environmental changes83,84. 406 
 407 
 408 
 409 
18 
 
Theme 6: How can we ‘manage’ microbiomes in the coastal environment and in association 410 
with hosts? 411 
  412 
Management or manipulation of microbial functions and communities are well-established 413 
techniques in bioremediation of terrestrial and aquatic ecosystems – for instance, those 414 
impacted by hydrocarbons and toxins contamination85. Principal approaches involve either 415 
biostimulation (the process of ‘activating’ indigenous microbes via, for example, nutrient 416 
amendments) or bioaugmentation (the process of inoculating the ecosystem with non-417 
indigenous microbes that have desired metabolic properties85), which have both been applied 418 
at ecosystem scales86,87. While these approaches have been less well-tested for marine 419 
systems, biostimulation strategies have been applied to deal with oil spills in ocean waters 420 
(e.g. Exxon Valdes or Deep Horizon disasters), primarily by supplying growth limiting 421 
nutrients, such as phosphate, to the site of contamination86. Biostimulation and 422 
bioaugmentation have also been used to accelerate degradation of polycyclic aromatic 423 
hydrocarbons in marine coastal sediments88.  424 
 425 
Host-associated microbial communities can also in principle be managed, as exemplified over 426 
the last few years by the development of sophisticated pre- and probiotic strategies for 427 
disease prevention and health improvement of humans, plants and some aquaculture 428 
species89-91. The advances in these hosts are facilitated in an increasingly detailed 429 
understanding of microbial diversity and functional processes, but such information is sparse 430 
for most natural marine hosts, thus preventing rational designs of pre- and probiotic 431 
strategies.62,92 Taken together, we envisage the following questions to be areas of increasing 432 
research: 433 
 434 
19 
 
● What are the key conditions to establish microbial-driven bioremediation processes in 435 
the coastal environment? 436 
● How does microbial manipulation in the early lifecycle stages of a host influence the 437 
performance and health of more mature host stages? 438 
● What is the role of microbial communities in facilitating the restoration of key hosts 439 
in impacted marine habitats? 440 
 441 
With the increasing urbanization of our coastlines and the increasing need to use polluted 442 
sites for recreational, private or commercial purposes, microbial-driven bioremediation will 443 
be one of the key tools to tackle this issue. Engagement and involvement of the local and 444 
regional stakeholders in the early stages of research will be essential for successful 445 
implementation. Additionally, as there is an increasing interest in developing probiotics or 446 
improving microbial symbiont function of important habitat-forming holobionts, global 447 
networks or initiatives, such as the Beneficial Microorganisms for Marine Organisms 448 
(BMMO), are powerful tools to progress this work, as has been shown for corals62,92. 449 
  450 
 451 
Theme 7: To what extent are coastal marine holobionts and their interactions with the 452 
environment relevant to human health and well-being? 453 
Coastal environments, including their associated biota, are the principal interface for human 454 
exposure to marine microbiomes and these interactions can sometimes have detrimental 455 
impacts on human health (Fig. 2). Human pathogens present within marine microbiomes 456 
include both indigenous marine microbes and enteric microbes that are exogenously 457 
introduced to coastal habitats via sewage and urban storm-water93 (Fig. 2). The microbiomes 458 
of benthic marine flora and fauna often display a high representation of marine pathogens - in 459 
20 
 
particular members of the Vibrio genus94. Several species within this genus are highly 460 
virulent and dangerous human pathogens, and in the USA alone are cumulatively responsible 461 
for health costs exceeding $250 million yr-1 95. In addition to native marine microbes, enteric 462 
pathogens that become, at least transiently, incorporated into marine microbiomes following 463 
exposure to coastal pollution also pose a significant health risk. Indeed, due to (i) the 464 
preference for coastal and estuarine habitats among many native marine pathogens94 and (ii) 465 
the regular exposure of coastal flora and fauna to human waste streams, the microbiomes of 466 
coastal organisms represent potentially important hotspots and reservoirs of human 467 
pathogens93 (Fig. 2). On the other hand, there is recent evidence that some marine macro-468 
organisms, specifically seagrasses, may act as effective natural filtration systems that remove 469 
human pathogens from coastal ecosystems, potentially through the production of biocides by 470 
the plant or its microbiome96 (Fig. 2).  471 
 472 
As the global human population rapidly increases its dependence and impact upon coastal 473 
environments97, it is imperative that we develop an understanding of the potential human 474 
health consequences of increasing contact with marine microbiomes. This is particularly true, 475 
given that there is emerging evidence that climate change and the anthropogenic degradation 476 
of coastal habitats are enhancing the occurrence and virulence of dangerous human pathogens 477 
within these ecosystems98 (Fig. 2). Within this specific context, we identify several key 478 
questions that remain unanswered, including: 479 
 480 
● Are potential human pathogens persistent or ephemeral members of the microbiomes 481 
of coastal organisms? 482 
● To what extent are environmental change and degradation enhancing the occurrence, 483 
persistence and virulence of human pathogens within coastal microbiomes? 484 
21 
 
● To what degree do enteric pathogens introduced to coastal microbiomes via human 485 
waste streams influence the health of the benthic coastal macro-organisms? 486 
 487 
New analytical approaches for interpreting microbiome data provide several opportunities to 488 
answer these questions. For instance the detection of novel “indicator” organisms99 or 489 
genes100 within microbiome data-sets delivers potentially powerful capacity to detect 490 
environmental perturbations and human contamination within coastal waters that goes far 491 
beyond standard indicators of human contamination (i.e. Faecal Indicator Bacteria [FIB]), 492 
which are often limited in sensitivity and explanatory power101. The analysis of coastal 493 
microbiome data also provides a facility to detect novel or emerging pathogens that are 494 
missed by standard FIB monitoring approaches102,103. Finally, the application of analytical 495 
approaches such as SourceTracker104 and random forest analyses105 allow for microbiome 496 
data to be directly used as a sensitive new tool for tracking sources of contamination or 497 
signals of environmental change. 498 
 499 
[suggested placement for Figure 2] 500 
[suggested placement for Box 3] 501 
 502 
Synthesis and Outlook  503 
Coastal marine microbiome research represents a direct pathway to understanding how 504 
microbes affect – both positively and deleteriously – the coastal ecosystems on which human 505 
populations so heavily rely. The themes and questions presented here, summarized in a 506 
conceptual framework (Fig. 3), include resolving the spatial, temporal, and evolutionary 507 
scales at which the holobionts and microbiomes function, resolving how holobionts change in 508 
response to environmental stimuli and each other, and determining the scope for how 509 
22 
 
microbiomes can be managed. Summarizing the future of coastal microbiome research 510 
through the horizon scan and literature survey has identified two overarching concepts 511 
common across the themes that reflect the current state of the science, as well as how we 512 
envision the science will progress: microbiome function and utilizing manipulative 513 
approaches.  514 
 515 
Defining microbiomes, either functionally or within the framework of a core microbiome, 516 
was a fundamental concept shared by all the themes. As outlined in Theme 1 and the 517 
literature survey, the field has made large strides in how we define microbiomes via 518 
taxonomic descriptions from amplicon sequencing. For some holobionts and ecosystems like 519 
mangrove and saltmarshes, gathering basic information on what microbiota are present and 520 
how they may be functioning is still lacking and would benefit from global-scale initiatives, 521 
such as recent efforts for seagrasses and sponges10,106. Conversely, the microbiome and 522 
holobiont systems that already have solid taxonomic foundations are looking to investigate 523 
how the microbiota function, alone and together with their hosts, in coastal marine 524 
ecosystems in order to answer the pressing ecological questions presented.  525 
 526 
Such investigations, as shown throughout the themes, are inherently complex, whereby the 527 
questions and concepts presented in one theme relied on the understanding of another theme. 528 
For example, teasing apart the relationship between microbiome and host health and 529 
resilience (Theme 4) depends on the temporal scale (Theme 2) and environmental conditions 530 
(Theme 5) that influence the interactions, but each of these themes in themselves also 531 
influence how microbiota are selected and form holobionts (Theme 3). The ever-changing 532 
nature of the ecological processes that influence the microbiomes and holobionts in the 533 
natural environment necessitates manipulative experimental approaches in order to tease 534 
23 
 
apart the questions presented. In some cases, such as the evolutionary, multi-stressor or 535 
management questions, highly controlled experiments are the best options currently available 536 
to progress the respective themes. Here, the use of model organisms may provide insight, for 537 
example, on selection mechanisms between host and microbe (Theme 3), and microbiome-538 
driven restoration (Theme 6). The large national and international collaborations or 539 
consortium efforts that have produced the descriptive data on environmental microbiomes to-540 
date, may be equally useful in progressing hypothesis-driven questions through concerted 541 
manipulative experimental approaches107, e.g. temperature effects on holobiont resilience at 542 
the biogeographic limits of the host (Themes, 5, 4 and 2, respectively) or how holobionts can 543 
act as sources or sinks of pathogenic microbiota under various point source or diffuse 544 
pollution scenarios (Theme 7). In summary, although the list of research themes we present 545 
here is broad and ambitious, the ongoing collaborative networks along with well-executed 546 
hypothesis-driven manipulative experiments are significantly progressing the definition and 547 
functional relationship between the core microbiome and host, illuminating global 548 
microbiome biogeography, and identifying key regional- and global-scale environmental 549 
influences on coastal marine microbiomes and holobionts. 550 
 551 
[suggested placement for Figure 3] 552 
 553 
Data availability: The original questions for the horizon scan are available in the 554 
supplementary materials. 555 
 556 
Code availability: The code used the extract literature from databases is available in the 557 
supplementary materials.  558 
24 
 
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Bioinformatics 34, 2371-2375, doi:10.1093/bioinformatics/bty113 (2018). 852 
116 Pogoreutz, C. et al. Nitrogen fixation aligns with nifH abundance and expression in 853 
two coral trophic functional groups. Frontiers in Microbiology 8, 1187 (2017). 854 
117 Cardini, U. et al. Microbial dinitrogen fixation in coral holobionts exposed to thermal 855 
stress and bleaching. Environmental microbiology 18, 2620-2633 (2016). 856 
118 Glasl, B., Herndl, G. J. & Frade, P. R. The microbiome of coral surface mucus has a 857 
key role in mediating holobiont health and survival upon disturbance. The ISME 858 
Journal 10, 2280–2292 (2016). 859 
119 Do Carmo, F. L. et al. Bacterial structure and characterization of plant growth 860 
promoting and oil degrading bacteria from the rhizospheres of mangrove plants. The 861 
Journal of Microbiology 49, 535 (2011). 862 
120 Bourlat, S. J. et al. Genomics in marine monitoring: new opportunities for assessing 863 
marine health status. Marine Pollution Bulletin 74, 19-31 (2013). 864 
 865 
  866 
30 
 
Correspondence and requests for materials should be addressed to S.T.T. 867 
 868 
Acknowledgements: 869 
We thank Deakin University’s School of Life and Environmental Sciences and the Centre for 870 
Integrative Ecology for funding the workshop (New Activities Scheme 2017). BL’s 871 
attendance at the workshop was funded by the New Zealand Ministry of Business, Innovation 872 
& Employment (MBIE) Smart Ideas project UOWX1602. LM’s attendance was supported 873 
by an Australian Research Council Discovery Project (DP160103811). AC’s attendance 874 
was funded by the Centre for Marine Bio-Innovation at UNSW Australia. AHE was 875 
supported by fellowship SFRH/BPD/107878/2015 from the Portuguese Science 876 
Foundation (FCT). DD was supported by King Abdullah University of Science and 877 
Technology (baseline research funds). STT was supported by Deakin University’s SEBE 878 
Postdoctoral Industry Fellowship, the Mary Collins Trust and the Alfred Deakin 879 
Postdoctoral Research Fellowship. We thank Jennifer Martiny, Steven Robbins, Gene 880 
Tyson, Claudia Weihe and Katrine Whiteson for their input in the horizon scanning 881 
exercise. We thank Leena Koop for producing the conceptual designs. 882 
 883 
 884 
Author Contributions: 885 
S.T.-T. conceived the idea; S.T.-T., C.S. and P.I.M. developed and led the workshop; S.T.-T., 886 
C.S., P.I.M., M.J.H., A.H.C., B.L., V.H.-M., J.S., L.M., T.A. and K.L.H. attended the 887 
workshop that structured the themes of the manuscript; S.T.-T., C.S., P.I.M., M.J.H., A.H.C., 888 
B.L., V.H.-M., J.S., L.M., T.A., K.L.H., A.F., D.D., S.E., A.H.E., M.F., T.T., L.V., A.H.-A., 889 
H.M.G., E.M.M. and P.D.S. contributed to the questions and wrote the manuscript; A.F., 890 
V.H.-M., S.T.-T. and L.H. contributed to the literature search. 891 
31 
 
 892 
The authors have no competing interests. 893 
  894 
32 
 
Figure Legends 895 
 896 
Fig. 1: Determining microbiome contribution to coastal ecosystem health. a. This paper on 897 
coastal marine microbiomes highlights six key holobionts that form the foundation of coastal 898 
ecosystems: corals, macroalgae, seagrasses, mangroves (sponges and saltmarshes not shown 899 
here). b. The core microbiome concept allows the identification of both persistent microbial 900 
phylotypes, and c. core functional roles played by microbes within holobionts, seawater and 901 
the sediment. Different microbes can constitute persistent microbiomes across varying 902 
spatial, temporal, organism and ecosystem scales (intersection in Venn diagram, b). 903 
However, these ubiquitous microbial communities are likely to present functional redundancy 904 
across coastal environments (similar relative abundance in functional genes, c), playing 905 
crucial roles in the functioning and health of coastal marine ecosystems. OTU = operational 906 
taxonomic unit, KEGG = Kyoto Encyclopedia of Genes and Genomes. Photo credits: coral 907 
reef: Alexander J. Fordyce; mangrove: Michael Bradley; seagrass and macroalgae: 908 
Pommeyrol Vincent and Ethan Daniels, respectively / Shutterstock. 909 
 910 
Fig. 2: Conceptual design of the potential relationships between coastal marine microbiomes 911 
and humans. (1) Coastal pollution, including stormwater and sewage effluence, introduce 912 
potentially pathogenic microbiota to coastal marine ecosystems. (2) Endemic marine 913 
pathogens, including Vibrio and toxic cyanobacteria, persist in coastal marine ecosystems. (3) 914 
Coastal aquaculture species can become contaminated by endemic and introduced pathogens, 915 
which can both (i) cause mortality, e.g. oysters, and (ii) have health implications for human 916 
consumers. (4) Endemic pathogens, e.g. Vibrio, can cause holobiont disease. (5) According to 917 
Lamb et al. 96, coastal macrophytes may act as natural pathogen filters, buffering the impact 918 
of pathogens for humans and coastal marine ecosystems. Climate change and CO2-mediated 919 
33 
 
pollution also represent major impacts that humans have on coastal microbiomes. These 920 
impacts, for example, may result in increased occurrence and virulence of pathogens like 921 
Vibrio via the warming of sea surface temperatures (2), and increased coastal pollution due to 922 
the greater frequency of storm events (1). The industry and global warming symbols are 923 
courtesy of the Integration and Application Network, University of Maryland Center for 924 
Environmental Science (ian.umces.edu/symbols/). 925 
 926 
Fig. 3: A conceptual diagram depicting several of the major research themes in coastal 927 
marine microbiome research. The diagram highlights several interactions that occur at 928 
multiple spatial levels. a. Using the macroalgae Ulva sp. as an example, the inset highlights 929 
six host-microbiome interactions and associations in relation to the ‘baseline’ holobiont 930 
(center host + microbiome). b, c. More broadly, the holobiont-scale of interactions and 931 
associations can also apply to large-scale or ecosystem-level scenarios, whereby the 932 
holobiont interacts with environmental microbiomes (e.g. sediments/substrates, seawater) and 933 
neighboring inter- and intra-species holobionts, while also being influenced by environmental 934 
or climatic conditions (not depicted here). 935 
  936 
34 
 
Boxes 937 
Box 1: Key Definitions 938 
Dysbiosis: An imbalance or disruption of the normally beneficial symbiotic relationship 939 
between the host and its associated microbiota. A dysbiotic microbiota may result in poor 940 
host health and/or reduced capacity for resistance to environmental perturbation. 941 
Holobiont: An ecological unit formed by a host and its associated microbiome(s). 942 
Horizon scanning: A technique used to systematically identify the gaps, challenges and 943 
opportunities in a field with the aim to outline future priorities and is often employed by 944 
eliciting the perspectives of experts in the field. 945 
Metagenomics: The study of microbial community structure, function and interactions 946 
through the sequencing and analysis of genetic material directly extracted from the 947 
environment. 948 
Metatranscriptomics: The study of the expressed genes in an environment or holobiont. 949 
Microbiome: The sum of the microbial consortia (and their genetic material) in an 950 
environment. The microbiome typically includes a diversity of prokaryotes (bacteria and 951 
archaea), eukaryotes (fungi and protozoa) and viruses. 952 
Operational taxonomic unit (OTU): Marker genes from multiple individuals that were 953 
clustered/grouped on the basis of sequence similarity to represent a taxonomic group. 954 
Phenotype: The observable characteristics of an organism, influenced by genetics and the 955 
environment. 956 
Phylogenetic marker genes: A genetic marker whose sequence is used to delineate 957 
taxonomic and evolutionary relationships. Examples are the 16S rRNA gene in 958 
prokaryotes and 18S rRNA gene and ITS (internal transcribed spacer regions) in 959 
eukaryotes. 960 
Quorum sensing: The ability to regulate gene expression in response to changes in cell-961 
population density through the production and detection of specific chemical signal 962 
molecules (autoinducers) within or among populations. 963 
 964 
 965 
 966 
 967 
 968 
35 
 
Box 2: Literature Search and Horizon Scan Methodology 969 
Approach: First, we surveyed the literature to identify the breadth of research to-date and 970 
evaluate the state of understanding in the field of coastal, estuarine, and marine microbiome 971 
research. A detailed description of the literature search, including the script that was used, 972 
can be found in Supplementary Methods. In brief, the SCOPUS database was used for 973 
searching, with keywords including: seagrass, mangrove, saltmarsh, macroalgae, coral, 974 
sponge, seaweed, seawater and sediment. This resulted in 671 publications, after irrelevant 975 
publications were excluded. We then manually scanned these publications to extract 976 
information on methods, host type, and GPS location of sampling site. The content of these 977 
papers was then used quantitatively and qualitatively in this paper to report on the state of the 978 
science.  979 
 980 
Second, we used a modified horizon scanning method108 to identify key questions in coastal 981 
marine microbiome research. This approach uses expert solicitation to provide strategic 982 
foresight into the key research gaps for future research; an approach that has been historically 983 
underutilized in environmental science109, yet can provide a powerful approach to prioritizing 984 
a research agenda when appropriately structured110,111. Briefly (more details provided in 985 
Supplementary Data 1), the approach involved asking experts in the field of microbiome 986 
research to freely contribute what they considered to be the most pending questions (10 987 
maximum) in coastal and estuarine microbiome science – i.e. what are the major research 988 
gaps and where do the challenges lie?  Experts were initially selected from within the lead 989 
and last author’s research networks and based on who the lead/last author perceived to be at 990 
the forefront of the research field through the aforementioned literature search. To this end, 991 
the selection of authors could be considered haphazard.  992 
 993 
A total of 34 experts were approached by email, spanning 12 institutions from Australia, 994 
Europe, Saudi Arabia and the United States (US). Of the invited experts, 28 experts (84%) 995 
contributed responses (after two email reminders) and submitted 108 questions collectively. 996 
A workshop was held at Deakin University (Melbourne, Australia) on 6-7 July 2017 to refine 997 
the questions based on the voting process as described in Sutherland et al. 108. The questions 998 
were grouped into major research themes and are presented herein to discuss the research 999 
gaps in the context of the questions that underpinned them. Therefore, the themes presented 1000 
below are not in a particular order of importance; they are arranged in a way that starts with 1001 
36 
 
microbiome-centric concepts, to relationships between microbiome and host, and lastly to 1002 
broader interactions within and across microbiomes, the holobiont and the environment (Box 1003 
Diagram). 1004 
 1005 
[suggested Box Diagram placement. Caption below] 1006 
Box Diagram: Conceptual design depicting the seven themes resulting from the horizon 1007 
scanning exercise.  1008 
 1009 
Limitations: Horizon scanning approaches have limitations, which, most importantly, 1010 
include the risk of questions being inherently biased by the interests of the researchers108. To 1011 
limit this bias, we made an effort to solicit questions from researchers across a wide range of 1012 
sub-fields, including plankton, sediment/substrate, seagrass, seaweed, coral, sponge and 1013 
mangrove microbiomes. Additionally, while the solicited scientists work internationally, we 1014 
were aware of potential biogeographic biases that could influence the questions. Therefore, in 1015 
the original request for questions, we asked the scientists to keep their questions global in 1016 
order to avoid national- or regional-specific topics. 1017 
 1018 
  1019 
37 
 
Box 3: Methodological challenges 
1. Molecular Approaches 
DNA and RNA sequencing has been increasingly used as the preferred technique in coastal marine 
microbiome studies (Supplementary Fig. 1), yet several challenges have the potential to limit the 
production of reliable datasets. Such molecular challenges are broadly found in microbiome research, so 
we outline two current challenges in coastal marine microbiome research and suggest promising 
techniques that could help overcome these issues: 
 Challenges Potential Solutions & Benefits 
 • Host genome 
contamination in 
(meta)genomic studies on 
host-associated 
microbiomes 
• Pre-and post-sequencing removal of contaminating host 
cells and DNA sequences via 
o Physical removal of host tissue, e.g. centrifugation, 
Percoll separation 
o In-silico removal of well-curated host DNA 
sequences post-sequencing 
o Removal of methylated eukaryotic host DNA*112  
o Host-specific blocking primers 
 Bioinformatic challenges  
• The level of taxonomic 
resolution needed in order 
to address questions on 
microbial composition and 
function 
 
• Employ amplicon sequencing approaches using universal 
primers as a first step (e.g. optimal gene segments V3 and 
V4), with added approaches, such as meta-‘omics’, for a 
more comprehensive understanding on microbial dynamics 
and functional roles. 
 • The arbitrarily defined 
97% sequence similarity 
designation of operational 
taxonomic units (OTUs) 
• Use the most up-to-date and statistically valid methods for 
inferring the highest taxonomic resolution, e.g. 113-115. 
Benefits include 
o Higher resolution profiles of microbial 
communities in a unit 
o Directly comparable between datasets 
o Genotype discrimination could also be improved 
by longer sequences 
2. Manipulative Experiments 
Laboratory manipulative experiments are key to addressing hypotheses in many of the research themes 
addressed here. Yet, while field microbiome experiments are essential to answer questions under natural, 
real-world conditions, field manipulations of host-microbiome interactions in coastal marine ecosystems 
are rare116,117. Challenges include the logistics of excluding prokaryotes in the environment e.g. 
sterilization or antibiotics, but, for holobionts that are easily transportable, could be overcome with 
antibiotic treatment in the laboratory before field deployment118. Such a combination of innovatively 
designed laboratory and field experiments likely hold the key to teasing out important microbiome and 
holobiont interactions. Experiments that exclude or add specific microbes, resources, or isotope tracers 
would be useful in understanding functions and fine-scale interactions (e.g. beneficial microbiota53), while 
the manipulation of environmental conditions could be used to simulate climate change, stress, or pollution 
scenarios (e.g. adding oil-degrading and plant growth promoting bacteria to oil spills in mangrove 
forests54,119). Additionally, large simulator laboratories and in situ manipulative experiments could be a 
potential middle ground for testing hypotheses that have inherent field challenges44. 
3. Coastal Marine Microbiome Management 
We discussed in Themes 4 and 6 the possibilities of managing and manipulating microbes in coastal 
marine ecosystems to aid in pollution and eutrophication remediation, restoration, disease management 
and enhancing host health and growth. With the current momentum in this space, we predict that several 
challenges and questions will arise, such as, ‘Can a managed or manipulated microbiome outlive its 
function, and if so, what impacts does this have on the microbiome, holobiont or ecosystem?’, ‘Is there a 
way to ‘stop’ a microbial function or remove a community once a particular job has been done?’, and 
‘How resilient would a managed or manipulated microbiome be to disturbances and how would they be 
monitored to know if a desirable or undesirable outcome is achieved?’. Lastly, we predict that one of the 
key challenges will be to incorporate applied microbiome research into local, regional and national policy 
and methodology. As Bourlat et al.120 also outlined, we suggest that stakeholders need to be identified and 
engaged at the state and national levels early on in the research. 
 
*This will lead to the removal of any methylated DNA including that from protists and occasionally fungi, 
depending on the methylation rate. 
38 
 
 1020 
Coral reefs Seagrasses
 Core/persistent microbiome = 3 shared OTUs
3
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Community A Community B
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 Core/persistent microbiome = 11 functions
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KEGG categories
MacroalgaeMangroves


Microbiome
1: Defining
2: Scale
Microbiome & Host
3: Assembly and disassembly
4: Resilience
Holobiont & Environment
5: Tripartite interactions
6: Management
7: Human connection