Shotgun metagenomics and microscopy indicate diverse cyanophytes, other bacteria, and microeukaryotes in the epimicrobiota of a northern Chilean wetland Nostoc (Cyanobacteria)

Abstract

Prokaryotic Nostoc, one of the world's most conspicuous and widespread algal genera (similar to eukaryotic algae, plants, and animals) is known to support a microbiome that influences host ecological roles. Past taxonomic characterizations of surface microbiota (epimicrobiota) of free‐living Nostoc sampled from freshwater systems employed 16S rRNA genes, typically amplicons. We compared taxa identified from 16S, 18S, 23S, and 28S rRNA gene sequences filtered from shotgun metagenomic sequence and used microscopy to illuminate epimicrobiota diversity for Nostoc sampled from a wetland in the northern Chilean Altiplano. Phylogenetic analysis and rRNA gene sequence abundance estimates indicated that the host was related to Nostoc punctiforme PCC 73102. Epimicrobiota were inferred to include 18 epicyanobacterial genera or uncultured taxa, six epieukaryotic algal genera, and 66 anoxygenic bacterial genera, all having average genomic coverage ≥90X. The epicyanobacteria Geitlerinemia, Oscillatoria, Phormidium, and an uncultured taxon were detected only by 16S rRNA gene; Gloeobacter and Pseudanabaena were detected using 16S and 23S; and Phormididesmis, Neosynechococcus, Symphothece, Aphanizomenon, Nodularia, Spirulina, Nodosilinea, Synechococcus, Cyanobium, and Anabaena (the latter corroborated by microscopy), plus two uncultured cyanobacterial taxa (JSC12, O77) were detected only by 23S rRNA gene sequences. Three chlamydomonad and two heterotrophic stramenopiles genera were inferred from 18S; the streptophyte green alga Chaetosphaeridium globosum was detected by microscopy and 28S rRNA genes, but not 18S rRNA genes. Overall, >60% of epimicrobial taxa were detected by markers other than 16S rRNA genes. Some algal taxa observed microscopically were not detected from sequence data. Results indicate that multiple taxonomic markers derived from metagenomic sequence data and microscopy increase epimicrobiota detection.

Genomic Insights on the Functional Capabilities of the Cyano-Sphere of Edible Andean Nostoc Macrocolonies (Llayta)

“…Vilo et al [23] have reported the identification and the draft genome of a Bacillus bacterium from the microbiota associated with Llayta colonies as a first approach to address physiological relationships within the Llayta microbiome and to gain insights on the survival and adaptive strategies to dryness, arsenic, and UV radiation, among other prevalent extreme environmental conditions at the Andes wetlands. The presence of Anabaena on the resilient microflora accompanying the filamentous Nostoc Llayta was coincident with previous observations reported on Nostoc colonies from Parinacota wetlands [22].…”

“…Conversely, a different bacterial composition was found at the inner matrix, outer layer, and the littoral zone on Nostoc macrocolonies from Chungará Lake in northern Chile [21]. Comparatively, and using metagenomics, multiple taxonomic markers, and microscopic approaches, Satjarak et al [22] reported high taxonomic diversity (cyanobacteria, microalgae, and anoxygenic bacterial genera) on the accompanying epimicrobiota of macroscopic dark-brown sheets of Nostoc from standing water pools at Parinacota (Lauca National Park, northern Chile).…”

“…Filaments accumulate into a mucilaginous matrix rich in a complex polysaccharide enclosed by an outer envelope in Nostoc species capable of forming macrocolony. Nostoc macrocolonies can be observed as sheet-like or spherical forms with green to brown colorations, depending upon the species, dehydration state, and local environment [17][18][19][20][21][22]32]. In natural environments, macrocolonies of filamentous diazotrophic Nostoc are colonized by diverse microorganisms involved in biogeochemical cycles and ecosystem services [33].…”

“…The natural life cycle of primary producers may involve mutualistic, antagonistic, or commensal interactions with cyanophages, fungi, and heterotrophic bacteria. Positive or negative outcomes from such interactions have been previously discussed in Nostoc macrocolonies [18,19] and reported in Andean Nostoc macrocolonies [20][21][22]. However, studies on identifying members of the bacterial community associated with edible Llayta macrocolonies have been a pending issue.…”

Metagenome-Assembled Genome of Cyanocohniella sp. LLY From the Cyanosphere of Llayta, an Edible Andean Cyanobacterial Macrocolony

“…The natural life cycle of primary producers may involve mutualistic, antagonistic, or commensal interactions with cyanophages, fungi, and heterotrophic bacteria, and positive or negative outcomes have been previously discussed in Nostoc macrocolonies [24][25][26][27]. However, identification of members of the bacterial community associated with edible Llayta macrocolonies have been a pending issue.…”