Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network

Abstract

Blooms of planktonic cyanobacteria have long been of concern in lakes, but more recently, harmful impacts of riverine benthic cyanobacterial mats been recognized. As yet, we know little about how various benthic cyanobacteria are distributed in river networks, or how environmental conditions or other associated microbes in their consortia affect their biosynthetic capacities. We performed metagenomic sequencing for 22 Oscillatoriales-dominated (Cyanobacteria) microbial mats collected across the Eel River network in Northern California and investigated factors associated with anatoxin-a producing cyanobacteria. All microbial communities were dominated by one or two cyanobacterial species, so the key mat metabolisms involve oxygenic photosynthesis and carbon oxidation. Only a few metabolisms fueled the growth of the mat communities, with little evidence for anaerobic metabolic pathways. We genomically defined four cyanobacterial species, all which shared <96% average nucleotide identity with reference Oscillatoriales genomes and are potentially novel species in the genus Microcoleus. One of the Microcoleus species contained the anatoxin-a biosynthesis genes, and we describe the first anatoxin-a gene cluster from the Microcoleus clade within Oscillatoriales. Occurrence of these four Microcoleus species in the watershed was correlated with total dissolved nitrogen and phosphorus concentrations, and the species that contains the anatoxin-a gene cluster was found in sites with higher nitrogen concentrations. Microbial assemblages in mat samples with the anatoxin-a gene cluster consistently had a lower abundance of Burkholderiales (Betaproteobacteria) species than did mats without the anatoxin-producing genes. The associations of water nutrient concentrations and certain co-occurring microbes with anatoxin-a producing Microcoleus motivate further exploration for their roles as potential controls on the distributions of toxigenic benthic cyanobacteria in river networks.

Multiple cyanotoxin congeners produced by sub-dominant cyanobacterial taxa in riverine cyanobacterial and algal mats

“…This is consistent with results from Anabaena cultures isolated, and Anabaena draft-genomes assembled from the Eel and Russian rivers (unpublished observations; K.B.G.). This study detected the anaC gene at sites where Bouma-Gregson et al [18] did not find anatoxin biosynthesis gene clusters in their metagenomes; however our results correspond with previous anatoxin detections in the upper reaches of the Eel watershed [16]. Bouma-Gregson et al [18] found that only one of four Microcoleus strains detected in the metagenomes contained the anatoxin biosynthesis gene cluster.…”

“…This study detected the anaC gene at sites where Bouma-Gregson et al [18] did not find anatoxin biosynthesis gene clusters in their metagenomes; however our results correspond with previous anatoxin detections in the upper reaches of the Eel watershed [16]. Bouma-Gregson et al [18] found that only one of four Microcoleus strains detected in the metagenomes contained the anatoxin biosynthesis gene cluster. The lack of anaC detections with the ddPCR at 1_ELD and 2_SFE despite anatoxins being present at very low concentrations likely reflects the difficulty in completely homogenising samples and highlights the sensitivity of LC-MS/MS as an analytical detection method for these toxins.…”

“…PCC 10601, PCC 9240; GenBank accession: JF803652, JF803653; 100% cover and 99.7% identity) and Phormidium autumnale (now Microcoleus autumnalis ; CAWBG618; GenBank accession: KX016036; 93% cover and 99.6% identity) from the Cawthron Institute Culture Collection of Microalgae (http://cultures.cawthron.org.nz/). Comparison of sequences from this study to draft metagenomes from Bouma-Gregson et al [18] revealed 100% nucleotide sequence identity with the anaC gene from the draft M. autumnalis genomes assembled in their study. The closest Anabaena sp.…”

“…Extensive mats dominated by the green alga C. glomerata , are often also present at these locations, with low levels of cyanobacteria in the mats. There is uncertainty about which genera in these systems are producing toxins, although Microcoleus has been identified as an anatoxin producer in the Eel River using assembled metagenomes [18], and cultures of Microcoleus isolated from the Russian River also produce anatoxins [19]. Both toxic and non-toxic genotypes occur in the genus Microcoleus , and these genotypes can be present at varying relative abundances in environmental mats [15, 20], resulting in considerable spatial variability in anatoxin concentrations of mats within short distances.…”

The rise of diversity in metabolic platforms across the Candidate Phyla Radiation

“…We compiled a large set of CPR genomes from metagenomes from several previous studies of various environments. We also binned an additional set of genomes from metagenomes previously generated from sediment from Rifle, Colorado , groundwater from Crystal Geyser (Probst et al, 2017(Probst et al, , 2018 , a cyanobacterial mat from the Eel River network in northern California (Bouma-Gregson et al, 2019) , and groundwater from a cold sulfide spring in Alum Rock, CA. Binning methods and taxonomic assignment followed Anantharaman et al (2016).…”