synthesis of cellulose, extracellular fibrils and specific attachment factors such as surface proteins that help bacteria aggregate and form colonies. Archaea Though archaea are traditionally thought of as extremophiles, microbes belonging to extreme environments, advances in metagenomics and gene sequencing reveal that archaea are ubiquitous, found in nearly any environment including the root microbiome. For example, root-colonizing archaea have been discovered in maize, rice, wheat, and mangroves. Methanogen and ammonium-oxidizing archaea are prevalent members of the root microbiome, especially in anaerobic soils and wetlands. Archaeal phyla found in the root microbiome include Euryarchaeota, Nitrososphaerota (formerly Thaumarchaeota), and Thermoproteota (formerly Crenarchaeota). The presence and relative abundance of archaea in various environments suggest that they likely play an important role in the root microbiome. Archaea have been found to promote plant growth and development, provide stress tolerance, improve nutrient uptake and protect against pathogens. For example, Arabidopsis thaliana colonized with an ammonia-oxidizing soil archaea, Nitrosocosmicus oleophilius, exhibited increased shoot weight, photosynthetic activity and immune response. Examination of microbial communities in soil and roots identify archaeal organisms and genes that occupy functions similar to that of to bacteria and fungi, such as auxin synthesis, protection against abiotic stress and nitrogen fixation. In some cases, key genes for plant growth and development, such as metabolism and cell wall synthesis, are more prevalent in archaea than bacteria. Archaeal presence in the root microbiome can also be affected by plant hosts, which can change the diversity, presence and health of archaeal communities. Viruses Viruses also infect plants via the roots, however to penetrate the root tissues they typically use vectors such as nematodes or fungi. Assembly mechanisms There is an ongoing debate regarding what mechanisms are responsible for assembling individual microbes into communities. There are two primary competing hypotheses. One is that "everything is everywhere, but the environment selects," meaning biotic and abiotic factors pose the only constraints, through natural selection, to which microbes colonize what environments. This is called the niche hypothesis, and its counterpart is the hypothesis that neutral processes, such as distance and geographic barriers to dispersal, control microbial community assembly when taxa are equally fit within an environment. In this hypothesis, differences between individual taxa in modes and reach of dispersal explain the differences in microbial communities of different environments. Most likely, both natural selection and neutral processes affect microbial community assembly, though certain microbial taxa may be more restricted by one