The microbiome of North Sea copepods

Gerdts, Gunnar; Brandt, Petra; Kreisel, Katja; Boersma, Maarten; Schoo, Katherina L.; Wichels, Antje

doi:10.1007/s10152-013-0361-4

Cited by 32 publications

(34 citation statements)

References 82 publications

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“…Our results demonstrate that copepod-associated microbial communities differ from ambient seawater communities in terms of overall diversity and structure of the microbial communities, as has been observed in previous studies (30,36,57) (Figure S6, S7). Deep and shallow copepod populations cluster into unique clades and demonstrate distinct relative abundance patterns of the microbial members, reflecting the significant differences in microbial community structure between active and diapausing copepods (Figure 3).…”

Section: Community Composition Of Copepods and Ambient Seawatersupporting

confidence: 85%

“…have been found on copepods including C. finmarchicus in previous studies (36,(57)(58)(59)70), but our approach of examining physiologically distinct individual copepods enabled the identification of those microbial members that stably and reproducibly associate with C.…”

Section: Discussionmentioning

confidence: 99%

“…Trimmomatic software (56) was used in paired-end mode to remove adaptor sequences, low quality sequences (phred score < 20 bp), and the first 12 bp of the 5' end of the read, which often contain a biased nucleotide composition due to nonrandom hexamer priming (57). Reads greater than 50 bp in length after quality trimming were retained for assembly, resulting in a total of 102 million reads for assembly.…”

Section: De Novo Transcriptome Assembly and Post-assembly Analysismentioning

confidence: 99%

“…The 25 members of the core microbiome are from diverse phyla, including Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes (Table S6). The top 4 most abundant OTUs within the core are classified at the genus level as Vibrio (seq16), Propionibacterium (seq13), and Acinetobacter (seq111, seq68), all of which have been previously isolated from copepod samples (57)(58)(59), and several of which have chitin-degrading members (60,61).…”

Section: Community Composition Of Copepods and Ambient Seawatermentioning

confidence: 99%

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Interactions between calanoid copepod hosts and their associated microbiota

Almada¹

2015

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Zooplankton, such as copepods, are highly abundant environmental reservoirs of many bacterial pathogens. Although copepods are known to support diverse and productive bacterial communities, little is understood about whether copepods are affected by bacterial attachment and whether they can regulate these associations through mechanisms such as the innate immune response. This thesis investigates the potential role that copepod physiology may play in regulating Vibrio association and the community structure of its microbiome. To this end, the intrinsic ability of oceanic copepod hosts to transcriptionally respond to mild stressors was first investigated. Specifically, the transcriptional regulation of several heat shock proteins (Hsps), a highly conserved superfamily of molecular chaperones, in the copepod Calanus finmarchicus was examined and demonstrated that Hsps are a conserved element of the copepod's transcriptional response to stressful conditions and diapause regulation. To then investigate whether copepod hosts respond to and regulate their microbiota, the transcriptomic response of an estuarine copepod Eurytemora affinis to two distinct Vibrio species, a free-living strain (V. ordalii 12B09) and a zooplankton specialist (V. sp. F10 9ZB36), was examined with RNA-Seq. Our findings provide evidence that the copepod E. affinis does distinctly recognize and respond to colonizing vibrios via transcriptional regulation of innate immune response elements and transcripts involved in maintaining cuticle integrity. Our work also suggests that association with E. affinis can significantly impact the physiology of Vibrio colonists. Finally, the interindividual variability of the C. finmarchicus microbiome was examined to identify how specifically and predictably bacterial communities assemble on copepods and whether host physiology influences the bacterial community structure. Our findings suggest that copepods have a predictable "core microbiome" that persists throughout the host's entrance into diapause, a dormancy period characterized by dramatic physiological changes in the host. However, diapausing and active populations harbor distinct flexible microbiomes which may be driven by factors such including the copepod's feeding history, body size, and bacterial interactions. This thesis work highlights the role of copepods as dynamic reservoirs of diverse bacterial communities and implicates copepod host physiology as an important contributor to the activity, abundance, and community structure of its microbiome.

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Section: Community Composition Of Copepods and Ambient Seawatersupporting

confidence: 85%

Section: Discussionmentioning

confidence: 99%

Section: De Novo Transcriptome Assembly and Post-assembly Analysismentioning

confidence: 99%

Section: Community Composition Of Copepods and Ambient Seawatermentioning

confidence: 99%

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Interactions between calanoid copepod hosts and their associated microbiota

Almada¹

2015

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“…here is a growing interest in how microscale features, including living phytoplankton cells, phytoplankton exudate, and detrital particles, affect bacterial diversity and activity (1)(2)(3). Within these microenvironments, particles are relatively well studied as they can be readily physically separated from free-living bacteria using filtration.…”

mentioning

confidence: 99%

Insensitivity of Diverse and Temporally Variable Particle-Associated Microbial Communities to Bulk Seawater Environmental Parameters

Yung

Ward

Davis

et al. 2016

Appl Environ Microbiol

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There is a growing recognition of the roles of marine microenvironments as reservoirs of biodiversity and as sites of enhanced biological activity and in facilitating biological interactions. Here, we examine the bacterial community inhabiting free-living and particle-associated seawater microenvironments at the Pivers Island Coastal Observatory (PICO). 16S rRNA gene libraries from monthly samples (July 2013 to August 2014) were used to identify microbes in seawater in four size fractions: >63 m (zooplankton and large particles), 63 to 5 m (particles), 5 to 1 m (small particles/dividing cells), and <1 m (free-living prokaryotes). Analyses of microbial community composition highlight the importance of the microhabitat (e.g., particle-associated versus free-living lifestyle) as communities cluster by size fraction, and the microhabitat explains more of the community variability than measured environmental parameters, including pH, particle concentration, projected daily insolation, nutrients, and temperature. While temperature is statistically associated with community changes in the <1-m and 5-to 1-m fractions, none of the measured bulk seawater environmental variables are statistically significant in the larger-particle-associated fractions. These results, combined with high particle-associated community variability, especially in the largest size fraction (i.e., >63 m), suggest that particle composition, including eukaryotes and their associated microbiomes, may be an important factor in selecting for specific particle-associated bacteria. IMPORTANCEBy comparing levels of particle-associated and free-living bacterial diversity at a coastal location over the course of 14 months, we show that bacteria associated with particles are generally more diverse and appear to be less responsive to commonly measured environmental variables than free-living bacteria. These diverse and highly variable particle-associated communities are likely driven by differences in particle substrates both within the water column at a single time point and due to seasonal changes over the course of the year.

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Feeding strategy and dietary preference shape the microbiome of epipelagic copepods in a warm nutrient‐impoverished ecosystem

et al. 2022

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Copepods provide a rich organic microenvironment allowing the settlement and proliferation of microorganisms, forming dynamic microbial hotspots in the oceans. Such symbiotic associations in the plankton were previously hypothesized to be especially developed in warm oligotrophic seas, as they may serve as alternative sources of nutrients in biologically poor waters. Aiming to better understand how copepod microbiomes are shaped in an oligotrophic sea, we characterized microbiota associated with three dominant coastal epipelagic copepod species in the ultra‐oligotrophic Eastern Mediterranean Sea using amplicon sequencing of the 16S rRNA gene. Our results show that copepod‐associated microbial communities were host‐specific rather than determined by seasonal environmental changes. In the filter‐feeding copepod with a tendency to herbivory, Temora stylifera, microbial diversity was low and relatively stable throughout the year. In contrast, omnivorous copepods, the ambush‐feeding Oithona nana, and the mixed‐feeding Centropages ponticus harbored more diverse microbiomes dominated by transient taxa. We suggest that filter‐feeding strategy and narrow food spectrum can limit copepod–microbe interactions, while the ambush and mixed feeding strategies combined with omnivory confer higher microbial diversity. Filter feeders may reduce the recruitment of opportunistic microbes by maintaining high fidelity associations, as indicated by the large number of core taxa in T. stylifera. We underline the importance of the copepod–microbe associations in nutrient‐impoverished ecosystems, based on predicted enrichment of nitrogen metabolism in the core microbiome, mostly during summer when the shallow coastal waters are nitrogen‐depleted.

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The microbiome of North Sea copepods

Cited by 32 publications

References 82 publications

Interactions between calanoid copepod hosts and their associated microbiota

Interactions between calanoid copepod hosts and their associated microbiota

Insensitivity of Diverse and Temporally Variable Particle-Associated Microbial Communities to Bulk Seawater Environmental Parameters

Feeding strategy and dietary preference shape the microbiome of epipelagic copepods in a warm nutrient‐impoverished ecosystem

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