Depictions of the tree of life have both scientific and cultural importance. In biology, trees serve as tools to organize and infer evolutionary relationships between organisms, genomes and genes. These depictions also highlight the staggering diversity of life on Earth, how much has been discovered, and how much remains unknown. In 2016, in one of the first issues of Nature Microbiology, we published ‘A new view of the tree of life’, a research article by Laura Hug and colleagues that incorporated genomes from thousands of cultured and uncultivated bacteria, archaea and eukaryotes and substantially expanded the tree of life1. Hug and colleagues’ tree revealed unprecedented diversity and the evolutionary dynamics of microbial lineages, especially in those lacking cultured representatives. This ‘new view’ of the tree clearly depicted that life on Earth is predominantly microbial and dominated by an enigmatic and little understood majority. The work raised questions about how these microorganisms interact with each other and function within biogeochemical cycles, their impact on the environment and on human health, and what diversity remains yet to be discovered. We present a Focus issue featuring a set of articles on microbial ecology that showcases recent progress made towards understanding the relationships between microbes, viruses and their ecosystems and shines a light on future research questions to guide the field in the years to come.

Credit: Alex Whitworth

One of the pressing issues in microbial ecology is that there is so much of life about which very little is known. The taxonomic and ecological diversity of viruses remains poorly understood in many systems, and specifically in soil. In a Perspective, Carreira and colleagues posit that soil viruses are unappreciated regulators of ecological interactions that span from the microbial level to higher trophic levels of multicellular organisms such as plants and animals. To conceptualize these interactions, the authors recommend borrowing organizing principles from food web dynamics, while also accounting for the unique physicochemical nature of soils, where labyrinthine pore networks and particles constrain interactions between hosts and viruses. Building a better understanding of how viruses fit into soil food webs could reveal how these dynamics affect carbon cycling, agriculture and primary productivity and soil health.

There is growing appreciation that microbial ecological interventions hold tremendous potential as tools to safeguard against biodiversity loss and to increase ecosystem resilience2. In a Correspondence, Cordovez and colleagues describe a microbiome-based restoration strategy for an iconic tree of the Galápagos Islands that is threatened by invasive plants. The giant daisy tree Scalesia is referred to as the ‘Darwin’s finch’ of the plant world because its species-level variations in size, leaf shape and floral characteristics enable adaptation to the diverse environments on Galapágos, which reportedly drew the naturalist’s attention. Cordovez and colleagues introduce the Scalesia Microbiome Project — part of a citizen science effort to characterize the genetics of all organisms on Galápagos — that aims to better understand plant–microbe interactions that could contribute to seed germination, growth and stress resilience, while also better understanding plant–microbe evolution.

Turning attention from land to the ocean, this issue also addresses the microbial ecology of coral reefs, ecological hotspots of marine biodiversity, which are currently undergoing another global bleaching event. In a Microbe Matters, Madeleine van Oppen discusses a career spent studying the microbial symbionts of corals, dinoflagellates in the family Symbiodiniaceae. These photosynthetic microbial partners help build the coral calcium carbonate skeleton and produce fixed carbon that feeds the host animal. Bleaching occurs when elevated water temperatures cause the expulsion of Symbiodiniaceae, events that are often followed by mass coral mortality. Research led by van Oppen and her team has shown that some strains of Symbiodiniaceae are more heat tolerant than others, and that the evolution of these adaptations can be hastened in the laboratory. There is some evidence that corals hosting heat-evolved symbionts have enhanced thermal tolerance, but more work is needed to assess the stability of engineered partnerships and how these ecological dynamics might play out in the wild.

In order to capitalize on, or co-opt, any ecological relationships, the crosstalk between host and symbiont or microbiome must be fully understood. In a Perspective, Porter and colleagues synthesize recent insights into how leguminous plants control rhizobia, their microbial partners. These nitrogen-fixing microbes either promote the growth of host plants or have no appreciable effect on growth. Legumes optimize this symbiotic relationship through molecular signals and the formation of host nodules and compartments. Porter and colleagues suggest that teasing apart the chemical and physical features of host control is key to efficient nutrient cycling and the agricultural sustainability of these ecologically and economically important plants. The same level of ecological understanding would probably benefit other threatened ecosystems, from tropical fisheries to thawing permafrost fields.

The taxonomic and functional diversity of microbes and their viruses, and the myriad ways they impact the environment, can complicate making sense of microbial ecology and its broader impacts. In a Perspective, Sher and colleagues argue that metabolic principles in single cells can be extrapolated out to help explain complex cell–cell interactions, ecosystem dynamics and even global processes. They lay the foundation for a ‘common language’ that could be used to better understand microbial metabolism at scale. This model-based approach could be instrumental in assessing the efficacy of microbiome-based interventions or applied to conceptualize the ecological roles of microbial communities.

Since the new view tree of life was published in 2016 (ref. 1), the microbial branches have continued to flourish and grow. A Comment from Laura Hug describes the public and scientific reception to the tree, and how it has changed in the intervening years, thanks to improved methods and increased computational capacity. Although the rate of discovery of previously unknown major branches on the tree of life has slowed, there is still work to be done when it comes to closing genomes or bringing isolates into culture. What has not changed is that the tree of life remains a powerful symbol of the ecological and evolutionary importance of microbes. As Hug writes, “Future trees may need to distinguish not only between cultured and uncultured lineages, but also between extant and extinct”. Our hope is that by championing the field of microbial ecology, we can contribute to safeguarding microbial diversity for the future.