Metagenomics reveals biogeochemical processes carried out by sediment microbial communities in a shallow eutrophic freshwater lake

Bo Kuang; Rong Xiao; Yanping Hu; Yaping Wang; Ling Zhang; Zhuoqun Wei; Junhong Bai; Kegang Zhang; Jacquelinne J Acuña; Milko A Jorquera; Wenbin Pan

doi:10.3389/fmicb.2022.1112669

Metagenomics reveals biogeochemical processes carried out by sediment microbial communities in a shallow eutrophic freshwater lake

Front Microbiol. 2023 Jan 11:13:1112669. doi: 10.3389/fmicb.2022.1112669. eCollection 2022.

Authors

Affiliations

¹ College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China.
² State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China.
³ Department of Environmental Science and Engineering, North China Electric Power University, Baoding, China.
⁴ Department of Chemical Sciences and Natural Resources, University of La Frontera, Temuco, Chile.

Abstract

Introduction: As the largest shallow freshwater lake in the North China Plain, Baiyangdian lake is essential for maintaining ecosystem functioning in this highly populated region. Sediments are considered to record the impacts of human activities.

Methods: The abundance, diversity and metabolic pathways of microbial communities in sediments were studied by metagenomic approach to reveal patterns and mechanism of C, N, P and S cycling under the threat of lake eutrophication.

Results: Many genera, with plural genes encoding key enzymes involved in genes, belonging to Proteobacteria and Actinobacteria which were the most main phylum in bacterial community of Baiyangdian sediment were involved in C, N, S, P cycling processes, such as Nocardioides (Actinobacteria), Thiobacillus, Nitrosomonas, Rhodoplanes and Sulfuricaulis (Proteobacteria).For instance, the abundance of Nocardioides were positively correlated to TN, EC, SOC and N/P ratio in pathways of phytase, regulation of phosphate starvation, dissimilatory sulfate reduction and oxidation, assimilatory sulfate reduction, assimilatory nitrate reduction and reductive tricarboxylic acid (rTCA) cycle. Many key genes in C, N, P, S cycling were closely related to the reductive citrate cycle. A complete while weaker sulfur cycle between SO₄ ^2- and HS^- might occur in Baiyangdian lake sediments compared to C fixation and N cycling. In addition, dissimilatory nitrate reduction to ammonia was determined to co-occur with denitrification. Methanogenesis was the main pathway of methane metabolism and the reductive citrate cycle was accounted for the highest proportion of C fixation processes. The abundance of pathways of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling in sediments with higher TN content was higher than those with lower TN content. Besides, Nocardioides with plural genes encoding key enzymes involved in nasAB and nirBD gene were involved in these pathways.

Discussion: Nocardioides involved in the processes of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling may have important effects on nitrogen transformation.

Keywords: Baiyangdian; biogeochemical processes; metagenomics; microbial community; sediment.