Collection |

The plant microbiome

The UN General Assembly proclaimed that 2020 is the International Year of Plant Health to recognize and protect plant health, and to raise awareness of the crucial role of plant health in ecosystem health, food security and human health. Plants host diverse microbial communities that are associated with plant roots, the phyllosphere, rhizosphere and the endosphere, and comprise bacteria, fungi, protists, nematodes and viruses. Numerous studies from different fields of research have expanded our knowledge of the complex interactions between the plant, the associated microbial communities as well as the environment, and provided insights into the ecology and functions of this co-association, including the appreciation that the plant microbiota is important for plant growth, fitness, stress resilience and health. Such an increased understanding opens up the possibility to harness plant-associated communities for sustainable plant production and agricultural practises and to protect plants from the effects of climate change and human activities that lead to a decrease in biodiversity and the spread of plant diseases. This Collection contains Reviews and Research articles from across the Nature group of journals that cover the latest advances in plant microbiome research, addressing critical knowledge gaps that need to be addressed, such as a better understanding of the assembly of the plant-associated microbial communities, their dynamics, metabolic interactions or functional properties.


Mycorrhizas are ubiquitous mutualistic symbioses established between plant roots and soil fungi. In this Review, Bonfante and colleagues explore the origin and evolution of mycorrhizal fungi, the diversity of their interactions with host plants and the potential of application of mycorrhizal symbioses in the development of sustainable agricultural and environmental strategies.

Review Article | | Nature Reviews Microbiology

Actinobacteria are versatile producers of bioactive natural products. In this Review, van Wezel and colleagues discuss ecological and genomic insights into the mechanisms governing natural product metabolism and how those insights can be translated into approaches for computational and experimental genome mining strategies that yield novel bioactive molecules, in particular antibiotics.

Review Article | | Nature Reviews Microbiology

Microbiome engineering has many potential applications, ranging from agriculture to medicine. In this Review, Lawson, McMahon and colleagues guide us through the design–build–test–learn cycle that has been successful in many disciplines and explain how it applies to microbiome engineering.

Review Article | | Nature Reviews Microbiology

The microbial majority with which we share Earth often goes unnoticed despite underlying major biogeochemical cycles and food webs, thereby taking a key role in climate change. This Consensus Statement highlights the importance of climate change microbiology and issues a call to action for all microbiologists.

Consensus Statement | Open Access | | Nature Reviews Microbiology

Microbial communities are not only of great importance in the human gut, but also play irreplaceable roles in sustaining plant growth and functions. In this Perspective, strategies to optimize microbiome usage in agroecosystems are proposed.

Perspective | | Nature Plants

This Perspective assesses the opportunities and challenges for synthetic biology in revolutionizing agriculture, and highlights the resources and approaches we need to remove the barriers and propel another Green Revolution.

Perspective | | Nature Plants

Contamination of agricultural soils by heavy metals and metalloids has severe consequences on human and ecosystem health. This Review discusses the sources of heavy metal(loid) contamination, the mechanisms by which these contaminants interact with biological and geochemical soil elements, and plant-based and microorganism-based remediation strategies.

Review Article | | Nature Reviews Earth & Environment

Emerging fungal and oomycete pathogens pose a significant risk to global food security. This Review summarizes factors affecting pathogen introduction and spread and current disease control strategies, and highlights the direction that research must take to face the challenge of emerging crop pathogens.

Review Article | | Nature Food


A global assessment of the structure and function of the crop microbiome is urgently needed for the development of effective and rationally designed microbiome technologies for sustainable agriculture. Such an effort will provide new knowledge on the key ecological and evolutionary interactions between plant species and their microbiomes that can be harnessed for increasing agriculture productivity.

Comment | | Nature Reviews Microbiology

In this Viewpoint article, several experts discuss the microbial contributions to climate change and consider the effects of global warming, extreme weather and other consequences of climate change on microbial communities in the ocean and soil, host–microbiota interactions and the global burden of infectious diseases and ecosystem processes, and they explore open questions and research needs.

Viewpoint | | Nature Reviews Microbiology


Mutations in genes involved in immune signalling and vesicle trafficking cause defects in the leaf microbiome of Arabidopsis thaliana that result in damage to leaf tissues, suggesting mechanisms by which terrestrial plants control the level and diversity of endophytic phyllosphere microbiota.

Article | | Nature

Quantifying bacterial load in plant leaves, the authors show that insect herbivory can cause compositional shifts in bacterial community structure, primarily by enhancing the growth of putative phytopathogens. Across a native host population, insect–bacteria co-infection load is highly clustered and associated with lower plant fitness.

Article | | Nature Ecology & Evolution

Analysing soil and rhizosphere microbial communities across a latitudinal gradient from southern to central Europe, the authors show that the belowground microbiomes of range-expanding plant species become more similar the further they are from their native range.

Article | | Nature Ecology & Evolution

The ecological niche of host-associated microbes is defined by both abiotic and biotic dimensions. Here the authors analyse published data on fungal and oomycete pathogens of plants, demonstrating that specialization can evolve independently on abiotic and biotic axes and that interactions with host plants reduce thermal niche breadth.

Article | Open Access | | Nature Communications