Microbial occurrence and symbiont detection in a global sample of lichen metagenomes

作者：Gulnara Tagirdzhanova, Paul Saary, Ellen S. Cameron, Carmen C. G. Allen, Arkadiy I. Garber, David Díaz-Escandón, A. Cook, Spencer Goyette, Veera Tuovinen Nogerius, Alfredo Passo, Helmut Mayrhofer, Håkon Holien, Tor Tønsberg, Lisa Y. Stein, ROBERT FINN, Toby Spribille · 发表于：PLoS Biology · 年份：2024 · DOI：10.1371/journal.pbio.3002862 · 被引用次数：42 · 研究领域：Lichen and fungal ecology、Mycorrhizal Fungi and Plant Interactions、Microbial Community Ecology and Physiology

In lichen research, metagenomes are increasingly being used for evaluating symbiont composition and metabolic potential, but the overall content and limitations of these metagenomes have not been assessed. We reassembled over 400 publicly available metagenomes, generated metagenome-assembled genomes (MAGs), constructed phylogenomic trees, and mapped MAG occurrence and frequency across the data set. Ninety-seven percent of the 1,000 recovered MAGs were bacterial or the fungal symbiont that provides most cellular mass. Our mapping of recovered MAGs provides the most detailed survey to date of bacteria in lichens and shows that 4 family-level lineages from 2 phyla accounted for as many bacterial occurrences in lichens as all other 71 families from 16 phyla combined. Annotation of highly complete bacterial, fungal, and algal MAGs reveals functional profiles that suggest interdigitated vitamin prototrophies and auxotrophies, with most lichen fungi auxotrophic for biotin, most bacteria auxotrophic for thiamine and the few annotated algae with partial or complete pathways for both, suggesting a novel dimension of microbial cross-feeding in lichen symbioses. Contrary to longstanding hypotheses, we found no annotations consistent with nitrogen fixation in bacteria other than known cyanobacterial symbionts. Core lichen symbionts such as algae were recovered as MAGs in only a fraction of the lichen symbioses in which they are known to occur. However, the presence of these and other micr...