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Chlamydiae represent a diverse group of obligate intracellular bacteria with elusive hosts in environmental settings. This study used one of the largest collections of wild amoebae (Dictyostelium discoideum and D. giganteum, 106 clones) collected over the past two decades to screen for novel environmental chlamydiae. We found that novel environmental chlamydiae are prevalent in two wild Dictyostelium species and assembled 42 novel chlamydiae metagenome-assembled genomes (MAGs). The MAGs represent three chlamydiae species previously only reported using 16S sequencing. Their genomes are divergent enough from other species to warrant placing them in two new genera (tentatively called Ca. Dictychlamydia sp. LF1, Ca. Dictychlamydia sp. LF2, and Ca. Feichlamydia sp. LF3). In addition, these chlamydiae species show strong host specificity with two Dictyostelium amoeba hosts, except one amoeba sample. Ca. Dictychlamydia sp. LF1 and Ca. Feichlamydia sp. LF3 was exclusively observed in D. discoideum, while Ca. Dictychlamydia sp. LF2 was found only in D. giganteum. Phylogenetic and comparative genomic analyses suggest that all three chlamydiae are close to arthropod-associated chlamydiae and likely have some intermediate characteristics between previously reported amoeba-associated and vertebrate-associated chlamydiae. This study significantly broadens our understanding of the chlamydial host range and underscores the role of amoebae as vital hosts for environmental chlamydiae. 

A key question in cooperation is how to find the right partners and maintain cooperative relationships. This is especially challenging for horizontally transferred bacterial symbionts where relationships must be repeatedly established anew. In the social amoeba Dictyostelium discoideum farming symbiosis, two species of inedible Burkholderia bacteria (Burkholderia agricolaris and Burkholderia hayleyella) initiate stable associations with naive D. discoideum hosts and cause carriage of additional bacterial species. However, it is not clear how the association between D. discoideum and its carried Burkholderia is formed and maintained. Here, we look at precisely how Burkholderia finds its hosts. We found that both species of Burkholderia clones isolated from D. discoideum, but not other tested Burkholderia species, are attracted to D. discoideum supernatant, showing that the association is not simply the result of haphazard engulfment by the amoebas. The chemotactic responses are affected by both partners. We find evidence that B. hayleyella prefers D. discoideum clones that currently or previously carried Burkholderia, while B. agricolaris does not show this preference. However, we find no evidence of Burkholderia preference for their own host clone or for other hosts of their own species. We further investigate the chemical differences of D. discoideum supernatants that might explain the patterns shown above using a mass spectrometry based metabolomics approach. These results show that these bacterial symbionts are able to preferentially find and to some extent choose their unicellular partners. In addition, this study also suggests that bacteria can actively search for and target phagocytic cells, which may help us better understand how bacteria interact with immune systems. 

A species can benefit or be hurt by other species. For example, honeybees and flowering plants help each other to flourish, while lions and gazelles behave in ways that decrease each other’s populations. Understanding these relationships is important for controlling pests and diseases. Sometimes it is easiest to study such interactions by looking at simple ones that happen on a small scale. Amoebas are common soil organisms that have the same basic organization as human cells. They are much larger and more complex than the bacteria that also live in the soil. How exactly the amoebas and bacteria interact in the soil is an important question, particularly as some of the bacteria can also live inside amoebas. Does this intimate relationship help or harm the amoeba? Shu, Brock, Geist et al. studied the relationship between a widely studied species of social amoeba and two species of bacteria that can live inside it. Some of the amoebas naturally contained one of the bacteria species, and others were infected with the bacteria in experiments. Throughout the entire life cycle of the amoebas, the bacteria lived inside them. During one part of the life cycle, amoebas form so-called fruiting bodies, which release spores that can develop into new amoebas. Shu et al. found that both types of bacteria alter the structure of the fruiting bodies in ways that reduce how well the spores disperse. One of the bacteria species, called Burkholderia hayleyella, harmed the amoebas a lot. It caused most harm to amoebas that do not naturally host the bacteria. This indicates that the amoebas that do host this species may have evolved to avoid its worst effects. The amoebas have many similarities to the white blood cells that clear bacteria from the human body. Certain bacteria can get inside white blood cells, causing diseases such as tuberculosis. Understanding how bacteria harm amoebas might be useful for understanding such diseases, and developing treatments for them. Though the bacteria Shu et al. studied are not toxic to humans, they are closely related to bacteria that are harmful. It is therefore possible that some bacteria that infect humans first evolve to infect amoebas.