Great Lakes Cladophora harbors phylogenetically diverse nitrogen‐fixing microorganisms

Abstract

Nitrogen‐fixing microorganisms are among the epiphytic communities in Cladophora, potentially benefitting the algae in nutrient‐deficient waters, but their abundance and diversity remain unexplored. In this study, we determined the abundance and taxonomic composition of these nitrogen‐fixing microorganisms in Cladophora growing on rocks, breakwall structures, or submerged dreissenid mussel beds around southern Lake Michigan (N = 33) during the summer 2015, using two complementary genomic techniques: quantitative PCR (qPCR) and shotgun metagenomic sequencing. Genomic DNA was extracted from processed algal pellets, and the nitrogen‐fixing microbes were quantified by qPCR by targeting the nifH gene. Mean nifH concentrations (log10 copy numbers/gram algae fresh weight ± SE) were 5.54 ± 0.09, ranging from 4.31 to 6.57. Mean nifH concentrations in water samples (log10 copy numbers/milliliter of water ± SE) were: 3.25 ± 0.06, ranging from 2.41 to 3.90. Shotgun sequencing of a subset of algal samples representing the four sampling locations (N = 10) revealed as many as 267 nifH reads from among the sequences of the 10 shotgun metagenomes (averaging 27 reads per metagenome), ranging from 5 to 91 reads from Jeorse Park (September) and North Beach (September) locations. Taxonomic assignment of nifH sequences identified members from bacteria and archaea domains showing a clear separation of reads at domain and lower taxonomic levels. Bacteria were relatively more abundant than archaea. Anabaena, Bradyrhizobium, Geobacter, Methylocystis, Oscillatoria sp., and Skermanella (all bacteria), and Methanoregula, Methanothrix, and Methanosarcina (archaea) were among the nitrogen‐fixing genera identified by the MEGAN Community Edition program. Collectively, these findings show that phylogenetically diverse nitrogen‐fixing microbial communities are part of the Cladophora microbiome, likely contributing to the algal nitrogen needs.

Differential Impacts of Road De-icers on Freshwater Bacterial Communities

“…The relative abundance of Devosia, another Gram− bacterium, was also increased in the HM samples, with members of this taxon known to tolerate brackish conditions [70]. Devosia can be associated with green algae which is consistent with its increased abundance as the chl a levels increased 3.4-fold, serving as a diazotroph by fixing nitrogen, but it can also facilitate the maintenance of ion homeostasis, which may be significant in the mixed salts of the "eco-friendly" de-icer [71,72]. Since members of Devosia can be halophilic and this genus was found at the highest relative abundance in the HM samples, we cannot exclude that it too was a contaminant in the M de-icer formulation.…”

Bioremediation of Nitrate in Agricultural Drainage Ditches: Impacts of Low-Grade Weirs on Microbiomes and Nitrogen Cycle Gene Abundance

“…In addition to the abundance of denitri cation functional genes, our CAP model revealed that the abundance of nitrogen xation gene (nifH) had a signi cant impact on the pattern of microbiome structures. Nitrogen xation is an energy-intensive process that typically occurs in N-de cient environments [10,56]. In this study, minimal nitrogen concentration was observed at the treatment outlet during low-ow seasons (e.g., 0.7 to 4.5 mg L -1 ), most likely due to the N removal by denitri cation and other anaerobic processes such as anammox.…”

“…The adoption of remediation programs and nutrient reduction policies, such as the European Green Deal and the Mississippi River Hypoxia Task Force [7,8], has created strong incentives for mitigation efforts. However, the anthropogenic inputs of nutrients, especially nitrogen and phosphorus, into watersheds still pose an imminent threat to global water quality [9,10].…”

Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand

“…Algal structural features, wide distribution, and ecological importance made the Cladophora microbiome a popular research topic during the past decade. Microbiome studies of the freshwater lacustrine Cladophora were conducted for algal samples collected from many locales, e.g., [4,6,[9][10][11][14][15][16][17][18][19][20]. However, the microbiomes of freshwater Cladophora living in lotic water bodies have not been investigated.…”