Dear Colleagues,

This Special Issue of MDPI’s Microorganisms focuses on the critically important interactions between the microbial community and aquatic organisms, including vertebrates, invertebrates, and plants.

Over the past 40 years, three trends have become operationally linked to one another—the enormous growth of the aquaculture industry, the decline of wild fisheries, and the contamination and destruction of habitats and ecosystems. Aquaculture is considered the fastest growing component in the food animal industry, expected to be valued at 270 billion USD by 2025 [1,2] having grown continuously over the past 40 years. In contrast, global fisheries have been in decline for 100 years [3–6], and marine and freshwater ecosystems have deteriorated or disappeared [7–10]. These trends have been, of course, driven by the dramatic increase in the human population, the commercial and humanitarian mandates to keep this population fed, and a disregard of ecosystem services in the pursuit of profit. Both aquaculture and wild fisheries are dependent on the successful recruitment of young fish through to breeding age and on wild feed stock for native fisheries. Regrettably, many aquatic populations and ecosystems have experienced degradation, sometimes severe, due to anthropogenic activities. In many cases, deteriorating ecosystems interrupt essential interactions between the microbial community and aquatic animals and plants. From an ecosystem perspective, all aquatic organisms (vertebrates, invertebrates, and plants) have co-evolved with their cognate aquatic microbial communities for millions of years, every aquatic animal and plant acquiring a microbiome unique to its population and local environment. Climate change is also impacting microbial communities of aquatic systems causing unnatural shifts in community structure. Climate change and anthropogenic pressures are often rapid and can disrupt co-evolved alliances between the microbial world and other aquatic biota. To better understand the potentially disastrous effects of these converging environmental factors on aquatic ecosystems, we propose a Special Issue focusing on the microbiome of aquatic animals and plants, including i.) the phylogenetic structure and function of the microbiomes of aquatic animals and plants in health and disease, ii.) the assembly of these microbiomes, iii.) the identification and characterization of pathogenic and probiotic strains and consortia, iv.) mechanisms of attachment of the microbiome, and v.) approaches that would enhance survival and recruitment of aquatic species through greater understanding of microbial communities in aquatic ecosystems.

1. Bostock, J., McAndrew, B.; Richards, R.; Jauncey, K.; Telfer, T.; Lorenzen, K.; Little, D.; Ross, L.; Handisyde, N.; Gatward, I.; et al. Aquaculture: global status and trends. Philos Trans R Soc Lond B Biol Sci, 2010, 365, 2897–2912.
2. Helmstetter, M. The Aquaculture Industry: An Ocean Of Investment Opportunity. Forbes
3. Christensen, V.; et al. A century of fish biomass decline in the ocean. Marine Ecology Progress Series, 2014, 512, 155–166.
4. Pauly, D. Beyond duplicity and ignorance in global fisheries. Ecological Dimensions for Sustainable Socio Economic Development 2013, 519–535.
5. Vasilakopoulos, P.; Maravelias, C.D.;Tserpes, G. The alarming decline of Mediterranean fish stocks. Biol. 2014, 24, 1643–1648.
6. Watson, R.A.; et al. Global marine yield halved as fishing intensity redoubles. Fish and Fisheries 2013, 14, 493–503.
7. Bond, N.R.; Lake, P.S.; Arthington, A.H. The impacts of drought on freshwater ecosystems: An Australian perspective. Hydrobiologia 2008, 600, 3–16.
8. Carpenter, S.R.; Stanley, E.H. and Vander Zanden, M.J. State of the World's Freshwater Ecosystems: Physical, Chemical, and Biological Changes. Annual Review of Environment and Resources, 2011, 36, 75–99.
9. Darwall, W.; et al. TheAlliance for Freshwater Life: A global call to unite efforts for freshwater biodiversity science and conservation. Aquatic Conservation: Marine and Freshwater Ecosystems 2018, 28, 1015–1022.
10. Saunders, M.I.; et al. Human impacts on connectivity in marine and freshwater ecosystems assessed using graph theory: A review. Marine and Freshwater Research 2016, 67.

Prof. Dr. Terence L. Marsh
Dr. Télesphore Sime-Ngando
Guest Editors

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