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. 2021 Sep 22;16(9):e0257017.
doi: 10.1371/journal.pone.0257017. eCollection 2021.

Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere

Alexa K Hoke  1 , Guadalupe Reynoso  1   2 , Morgan R Smith  1   3 , Malia I Gardner  1 , Dominique J Lockwood  1 , Naomi E Gilbert  1   4 , Steven W Wilhelm  4 , Isabella R Becker  1 , Grant J Brennan  1 , Katherine E Crider  1 , Shannon R Farnan  1 , Victoria Mendoza  1 , Alison C Poole  1 , Zachary P Zimmerman  1 , Lucy K Utz  1 , Louie L Wurch  1 , Morgan M Steffen  1
Affiliations

Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere

Alexa K Hoke et al. PLoS One. .

Abstract

Microbial interactions in harmful algal bloom (HAB) communities have been examined in marine systems, but are poorly studied in fresh waters. To investigate HAB-microbe interactions, we isolated bacteria with close associations to bloom-forming cyanobacteria, Microcystis spp., during a 2017 bloom in the western basin of Lake Erie. The genomes of five isolates (Exiguobacterium sp. JMULE1, Enterobacter sp. JMULE2, Deinococcus sp. JMULE3, Paenibacillus sp. JMULE4, and Acidovorax sp. JMULE5.) were sequenced on a PacBio Sequel system. These genomes ranged in size from 3.1 Mbp (Exiguobacterium sp. JMULE1) to 5.7 Mbp (Enterobacter sp. JMULE2). The genomes were analyzed for genes relating to critical metabolic functions, including nitrogen reduction and carbon utilization. All five of the sequenced genomes contained genes that could be used in potential signaling and nutrient exchange between the bacteria and cyanobacteria such as Microcystis. Gene expression signatures of algal-derived carbon utilization for two isolates were identified in Microcystis blooms in Lake Erie and Lake Tai (Taihu) at low levels, suggesting these organisms are active and may have a functional role during Microcystis blooms in aggregates, but were largely missing from whole water samples. These findings build on the growing evidence that the bacterial microbiome associated with bloom-forming algae have the functional potential to contribute to nutrient exchange within bloom communities and interact with important bloom formers like Microcystis.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Percent of annotated genes in each Subsystems (SEED) category.
Subsystem coverage for each of the isolates was 30% for Exiguobacterium sp. JMULE1, 33% for Enterobacter sp. JMULE2, 23% for Deinococcus sp. JMULE3, 26% for Paenibacillus sp. JMULE4, and 31% for Acidovorax sp. JMULE5.
Fig 2
Fig 2. Phylogenetic tree of bacterial homologues of indolepyruvate decarboxylase (IpdC).
Clusters are based on similarity to sequences of known function, specifically indolepyruvate decarboxylase (Group I), α-keto decarboxylase (Group II), acetolactate synthase (Group III), and phenylpyruvate decarboxylase (Group IV). Sequence alignment (527 amino acids) was performed using T-coffee (Notredame et al., 2000; Di Tomasso et al., 2011) and the Neighborhood-Joining phylogenetic tree was generated in Mega X (Kumar et al., 2018) with a bootstrap test of phylogeny (1000).
Fig 3
Fig 3. Proposed mechanisms of interaction in the Microcystis phycosphere.
The genomes of the five sequenced Lake Erie isolates indicate the genetic potential for bidirectional exchange of nutrients and other compounds with Microcystis colonies.
See this image and copyright information in PMC

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