Deciphering microeukaryotic-bacterial co-occurrence networks in coastal aquaculture ponds

Xiafei Zheng; Kui Xu; Jonathan Naoum; Yingli Lian; Bo Wu; Zhili He; Qingyun Yan

doi:10.1007/s42995-022-00159-6

Deciphering microeukaryotic-bacterial co-occurrence networks in coastal aquaculture ponds

Mar Life Sci Technol. 2023 Feb 22;5(1):44-55. doi: 10.1007/s42995-022-00159-6. eCollection 2023 Feb.

Authors

Xiafei Zheng^{1

2}, Kui Xu^{2

3}, Jonathan Naoum⁴, Yingli Lian^{2

5}, Bo Wu², Zhili He², Qingyun Yan²

Affiliations

¹ Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, 315100 China.
² Environmental Microbiomics Research Center, School of Environmental Science and Engineering, State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China.
³ Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization Technology, College of Life Sciences, Hubei Normal University, Huangshi, 435002 China.
⁴ Department of Biological Sciences, Ecotoxicology of Aquatic Microorganisms Laboratory, GRIL-EcotoQ-TOXEN, Université Du Québec À Montréal, Succursale Centre-Ville, Montreal, QC Canada.
⁵ Animal Husbandry and Fisheries Research Center of Guangdong Haid Group CO., Ltd. Key Laboratory of Microecological Resources and Utilization in Breeding Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, 510006 China.

Abstract

Microeukaryotes and bacteria are key drivers of primary productivity and nutrient cycling in aquaculture ecosystems. Although their diversity and composition have been widely investigated in aquaculture systems, the co-occurrence bipartite network between microeukaryotes and bacteria remains poorly understood. This study used the bipartite network analysis of high-throughput sequencing datasets to detect the co-occurrence relationships between microeukaryotes and bacteria in water and sediment from coastal aquaculture ponds. Chlorophyta and fungi were dominant phyla in the microeukaryotic-bacterial bipartite networks in water and sediment, respectively. Chlorophyta also had overrepresented links with bacteria in water. Most microeukaryotes and bacteria were classified as generalists, and tended to have symmetric positive and negative links with bacteria in both water and sediment. However, some microeukaryotes with high density of links showed asymmetric links with bacteria in water. Modularity detection in the bipartite network indicated that four microeukaryotes and twelve uncultured bacteria might be potential keystone taxa among the module connections. Moreover, the microeukaryotic-bacterial bipartite network in sediment harbored significantly more nestedness than that in water. The loss of microeukaryotes and generalists will more likely lead to the collapse of positive co-occurrence relationships between microeukaryotes and bacteria in both water and sediment. This study unveils the topology, dominant taxa, keystone species, and robustness in the microeukaryotic-bacterial bipartite networks in coastal aquaculture ecosystems. These species herein can be applied for further management of ecological services, and such knowledge may also be very useful for the regulation of other eutrophic ecosystems.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-022-00159-6.

Keywords: Bipartite network; Interactions; Keystone taxa; Microeukaryote; Nestedness.