Biodiversity of cyanobacteria and other aquatic microorganisms across a freshwater to brackish water gradient determined by shotgun metagenomic sequencing analysis in the San Francisco Estuary, USA

Abstract

Blooms of Microcystis and other harmful cyanobacteria can degrade water quality by producing cyanotoxins or other toxic compounds. The goals of this study were (1) to facilitate understanding of community structure for various aquatic microorganisms in brackish water and freshwater regions with emphasis on cyanobacteria, and (2) to test a hypothesis that Microcystis genotypes that tolerate higher salinity were blooming in brackish water environments during the severe drought, 2014. Shotgun metagenomic analysis revealed that cyanobacteria dominated the brackish water region while bacteria dominated the freshwater region. A group of cyanobacteria (e.g., Aphanizomenon, Microcystis, Planktothrix, Pseudanabaena), bacteria (e.g., Bacillus, Porphyrobacter), and diatoms (Phaeodactylum and Thalassiosira) were abundant in the brackish water region. In contrast, Hassallia (cyanobacteria) and green algae (Nannochloropsis, Chlamydomonas, and Volvox) were abundant in the landward freshwater region. Station variation was also apparent. One landward sampling station located downstream of an urbanized area differed substantially from the other stations in terms of both water chemistry and community structure, with a higher percentage of arthropods, green algae, and eukaryotes. Screening of the Microcystis internal transcribed spacer region revealed six representative genotypes, and two of which were successfully quantified using qPCR (Genotypes I and VI). Both genotypes occurred predominantly in the freshwater region, so the data from this study did not support the hypothesis that salinity tolerant Microcystis genotypes bloomed in the brackish water region in 2014.

Analysis of Covalently Bound Microcystins in Sediments and Clam Tissue in the Sacramento–San Joaquin River Delta, California, USA

“…This is consistent with previous work, which showed that the San Joaquin River had higher concentrations of Microcystis and higher concentrations of MCs in the algal fraction compared to surrounding regions of the Delta [40,43,54]. Toxin producing Microcystis was also detected at multiple sampling sites in the San Joaquin River [55]. The San Joaquin River water quality is more conducive to Microcystis blooms, with higher summertime temperatures and nutrient concentrations than surrounding regions.…”

A pilot study of the performance of captive‐reared delta smelt Hypomesus transpacificus in a semi‐natural environment

“…Gut contents of dead fish were collected and pooled monthly, preserved with ethanol (200 proof, Koptec, King of Prussia, PA) and used for identification of prey items by shotgun metagenomic sequencing analysis (Kurobe et al ., ; Jovel et al ., ). After quality trimming and concatenating pair‐end sequences, we obtained a total of 15 million DNA sequences with an average length of 398 bp for the six libraries (Supporting Information Table S1).…”

Salt Shock Responses of Microcystis Revealed through Physiological, Transcript, and Metabolomic Analyses

“…As a consequence, the accumulation of transferred MCs was described in marine fauna such as sea otters and shellfish [11][12][13]. The occurrence of M. aeruginosa and/or MCs in brackish waters was reported in many locations in the United States, South America, Australia, Europe including France, Japan, or India [14][15][16][17][18][19][20] and even became recurrent in San Francisco Bay, USA [21] and in the Patos Lagoon, Brazil [22]. Long-term survey and model predictions pointed out the positive impact of climate change on the intensity and frequency of this phenomenon through the intensification of precipitation and longer drought periods [15,16,23,24].…”