Seasonal variation in the copepod gut microbiome in the subtropical North Atlantic Ocean

Abstract

Characterisation of marine copepod gut microbiome composition and its variability provides information on function of marine food webs, biogeochemical cycles and copepod health. Copepod gut microbiomes were investigated quarterly over two years at the Bermuda Atlantic Time-series Station in the North Atlantic Subtropical Gyre, while assessing seasonal shifts in stable and transient communities. Microbial communities were analysed using amplicon sequencing targeting the bacterial 16S rRNA V3-V4 region and the cyanobacterial ntcA gene. Persistent bacterial groups belonging to Firmicutes, Bacteroidetes and Actinobacteria were present in the copepod guts throughout the year, and showed synchronous changes, suggesting a link to variability in copepod nutritional content. The gut communities were separate from those in the seawater, suggesting the copepod gut hosts long-term, specialized communities. Major temporal variations in the gut communities during the early winter and spring, specifically a high relative abundance of Synechococcus (up to 65%), were attributed to bacterioplankton shifts in the water column, and copepod grazing on these picoplanktonic cyanobacteria. The presence of obligate and facultative anaerobes, including Clostridiales year round, suggests that anaerobic bacterial processes are common in these dynamic microhabitats in the oligotrophic open ocean.

Mercury-methylating bacteria are associated with copepods: A proof-of-principle survey in the Baltic Sea

“…Furthermore, a better understanding of community structure is needed. Although our results do not provide any taxonomic identification of the bacteria involved, the observed prevalence of Firmicutes among the hgcA-carriers (Fig 1) agrees well with a relatively high abundance of this bacterial group in the microbiome of other copepods [28,29]. In future studies, a 16S rRNA gene diversity profiling and hgcAB amplification with high-throughput sequencing should be combined with hgcA quantification [11].…”

Copepods promote bacterial community changes in surrounding seawater through farming and nutrient enrichment

“…Among the zoosphere groups that were the most abundant in seawater were Rhodobacteriaceae (11% of the seawater community in this study) and Halomonadaceae (8.5% of the seawater community). Flavobacteriaceae, a dominant zoosphere group, did not grow well in the seawater incubations, but is routinely found in the surface layers at Bermuda Atlantic Time Series Station (BATS; 5%–17% of the seawater community seasonally; Shoemaker and Moisander, ). This group is often associated with marine snow and phytoplankton (Kirchman, ; Buchan et al ., ).…”

“…The V3-V4 region of the 16S rRNA gene was amplified by bacteria-specific primers, Bact-0341F/Bact-0785R (Klindworth et al, 2013). Amplicon libraries were created following a previously published protocol (Shoemaker and Moisander, 2017). Pairedend sequencing was performed at the Tufts University Core Facility for Genomics (Boston, MA) using the Illumina MiSeq v300 method.…”

Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes

“…In contrast, it has been shown that Firmicutes, Bacteroidetes and Actinobacteria are the most dominant members of the bacterial community associated with copepods in the North Atlantic Ocean (De Corte et al, 2014;Shoemaker and Moisander, 2017). This variation of the bacterial community associated with copepods may be caused by different trophic status (eutrophic lakes vs. oligotrophic marine environments) and seasonal differences (Shoemaker and Moisander, 2017). The phylum Bacteroidetes, especially the members of Flavobacteria, is highly abundant in the zooplankton-associated community which may play a crucial role in the degradation of high molecular weight organic matter (e.g., cellulose and chitin), proteins, and diatom debris (Qi et al, 2009;Buchan et al, 2014;Yang et al, 2015).…”

“…Other microbiome studies of cladocerans (e.g., Daphnia) showed the presence of these two dominant phyla (Qi et al, 2009;Freese and Schink, 2011). In contrast, it has been shown that Firmicutes, Bacteroidetes and Actinobacteria are the most dominant members of the bacterial community associated with copepods in the North Atlantic Ocean (De Corte et al, 2014;Shoemaker and Moisander, 2017). This variation of the bacterial community associated with copepods may be caused by different trophic status (eutrophic lakes vs. oligotrophic marine environments) and seasonal differences (Shoemaker and Moisander, 2017).…”