The water depth-dependent co-occurrence patterns of marine bacteria in shallow and dynamic Southern Coast, Korea

Abstract

To investigate the interactions between bacterial species in relation to the biotic and abiotic environmental fluctuations, free-living (FL), nanoparticle-associated (NP), and microparticle-associated (MP) bacterial community compositions (BCCs) were analyzed. A total of 267 samples were collected from July to December 2016 in the dynamic and shallow southern coastal water of Korea. The variations in BCC mostly depended on planktonic size fraction. Network analysis revealed water depth-dependent co-occurrence patterns of coastal bacterial communities. Higher interspecies connectivity was observed within FL bacteria than NP/MP bacteria, suggesting that FL bacteria with a streamlined genome may need other bacterial metabolites for survival, while the NP/MP copiotrophs may have the self-supporting capacity to produce the vital nutrients. The analysis of topological roles of individual OTUs in the network revealed that several groups of metabolically versatile bacteria (the marine Roseobacters, Flavobacteriales, Desulfobacterales, and SAR406 clade) acted as module hubs in different water depth. In conclusion, interspecies interactions dominated in FL bacteria, compared to NP and MP bacteria; modular structures of bacterial communities and keystone species strongly depended on the water depth-derived environmental factors. Furthermore, the multifunctional, versatile FL bacteria could play pivotal roles in dynamic shallow coastal ecosystems.

Figure 1

A heatmap of the 10 most enriched families in each sample. Average values of families within each fraction from different water depths are listed. Surf, surface; Mid, middle depth; Bot, bottom depth.

Figure 2

Distance-based redundancy analysis (db-RDA) in the FL (a), NP (b), and MP (c) fractions. All three db-RDAs and environmental parameters included were statistically significant (P < 0.001).

Figure 3

Correlation-based co-occurrence networks for each month. The size of each node is proportional to the number of connections (i.e., degree). Different colors indicate different modules in each month.

Figure 4

Ternary plots of bacterial OTUs in different modules with reference on the water depth (a) and bacterial composition (class level) of major modules in different water depths (b). Different colors indicate different modules. Modules composed of the OTUs dominating in surface were shaded with pink ovals, middle and bottom depth with gray ovals. Surf., surface depth; Mid.&Bot., middle and bottom depth; All, all depths.

Figure 5

The recurrence-based network constructed with correlations observed more than 3 times in monthly networks (edge color: 3 times, blue lines; 4 times, green lines; 5 times, red lines). The order name of an OTU is denoted in the node. The size of each node is proportional to the average degree over five months (monthly networks). OTUs are colored by phylum level. Module hubs are marked with thick black outlines.

Figure 6

Plot of within-module degree (Z) and among-module connectivity (C). The threshold values of Z and C for categorizing OTUs were 1.5 and 0.62. The different colors indicate that OTUs were more abundant at specific water depths: red, surface depth; blue, middle and bottom depth; green, whole depths. The symbol size is proportional to the node degree.