Inter-individual variability in copepod microbiomes reveals bacterial networks linked to host physiology

Datta, Manoshi Sen; Almada, Amalia A; Baumgartner, Mark F.; Mincer, Tracy J.; Tarrant, Ann M.; Polz, Martin F.

doi:10.1038/s41396-018-0182-1

Cited by 51 publications

(53 citation statements)

References 53 publications

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“…The zoosphere‐associated bacteria are among the most commonly reported bacteria in copepods (Shoemaker and Moisander, ; Datta et al ., ). These groups are also regularly reported from oceanic particle‐associating bacterial communities (López‐Pérez et al ., ; Pelve et al ., ).…”

Section: Discussionmentioning

confidence: 97%

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

Shoemaker

Duhamel

Moisander

2019

Environmental Microbiology

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Summary Bacteria living in the oligotrophic open ocean have various ways to survive under the pressure of nutrient limitation. Copepods, an abundant portion of the mesozooplankton, release nutrients through excretion and sloppy feeding that can support growth of surrounding bacteria. We conducted incubation experiments in the North Atlantic Subtropical Gyre to investigate the response of bacterial communities in the presence of copepods. Bacterial community composition and abundance measurements indicate that copepods have the potential to influence the microbial communities surrounding and associating with them – their ‘zoosphere’, in two ways. First, copepods may attract and support the growth of copiotrophic bacteria including representatives of Vibrionaceae, Oceanospirillales and Rhodobacteraceae in waters surrounding them. Second, copepods appear to grow specific groups of bacteria in or on the copepod body, particularly Flavobacteriaceae and Pseudoalteromonadaceae, effectively ‘farming’ them and subsequently releasing them. These distinct mechanisms provide a new view into how copepods may shape microbial communities in the open ocean. Microbial processes in the copepod zoosphere may influence estimates of oceanic bacterial biomass and in part control bacterial community composition and distribution in seawater.

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Section: Discussionmentioning

confidence: 97%

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

Shoemaker

Duhamel

Moisander

2019

Environmental Microbiology

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“…Copepods (Subphylum Crustacea; Class Hexanauplia; Subclass Copepoda) are an abundant and diverse group of zooplankton in the ocean 1 , 2 . They play a key role in energy transfer within the pelagic food web 3 .…”

Section: Introductionmentioning

confidence: 99%

Meta-analysis cum machine learning approaches address the structure and biogeochemical potential of marine copepod associated bacteriobiomes

Sadaiappan

PrasannaKumar

Nambiar

et al. 2021

Sci Rep

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Copepods are the dominant members of the zooplankton community and the most abundant form of life. It is imperative to obtain insights into the copepod-associated bacteriobiomes (CAB) in order to identify specific bacterial taxa associated within a copepod, and to understand how they vary between different copepods. Analysing the potential genes within the CAB may reveal their intrinsic role in biogeochemical cycles. For this, machine-learning models and PICRUSt2 analysis were deployed to analyse 16S rDNA gene sequences (approximately 16 million reads) of CAB belonging to five different copepod genera viz., Acartia spp., Calanus spp., Centropages sp., Pleuromamma spp., and Temora spp.. Overall, we predict 50 sub-OTUs (s-OTUs) (gradient boosting classifiers) to be important in five copepod genera. Among these, 15 s-OTUs were predicted to be important in Calanus spp. and 20 s-OTUs as important in Pleuromamma spp.. Four bacterial s-OTUs Acinetobacter johnsonii, Phaeobacter, Vibrio shilonii and Piscirickettsiaceae were identified as important s-OTUs in Calanus spp., and the s-OTUs Marinobacter, Alteromonas, Desulfovibrio, Limnobacter, Sphingomonas, Methyloversatilis, Enhydrobacter and Coriobacteriaceae were predicted as important s-OTUs in Pleuromamma spp., for the first time. Our meta-analysis revealed that the CAB of Pleuromamma spp. had a high proportion of potential genes responsible for methanogenesis and nitrogen fixation, whereas the CAB of Temora spp. had a high proportion of potential genes involved in assimilatory sulphate reduction, and cyanocobalamin synthesis. The CAB of Pleuromamma spp. and Temora spp. have potential genes accountable for iron transport.

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“…Some of these bacteria had the capacity to deactivate soybean chemical defenses, suggesting that the insects are able to maintain potentially valuable bacterial partners in their gut during diapause. Marine copepod microbiota are highly variable from individual to individual but undergo some predictable changes when the copepods stop feeding and enter diapause (Datta et al, 2018). Specifically, bacterial taxa associated with Figure 1.…”

Section: Changes In Microbiome Composition During Diapausementioning

confidence: 99%

Animal-Microbe Interactions in the Context of Diapause

Mushegian

Tougeron

2019

The Biological Bulletin

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Dormancy and diapause are key adaptations in many organisms, enabling survival of temporarily or seasonally unsuitable environmental conditions. In this review, we examine how our understanding of programmed developmental and metabolic arrest during diapause intersects with the increasing body of knowledge about animal co-development and co-evolution with microorganisms. Host-microbe interactions are increasingly understood to affect a number of metabolic, physiological, developmental, and behavioral traits and to mediate adaptations to various environments. Therefore, it is timely to consider how microbial factors might affect the expression and evolution of diapause in a changing world. We examine how a range of host-microbe interactions, from pathogenic to mutualistic, may have an impact on diapause phenotypes. Conversely, we examine how the discontinuities that diapause introduces into animal host generations can affect the ecology of microbial communities and the evolution of host-microbe interactions. We discuss these issues as they relate to physiology, evolution of development, local adaptation, disease ecology, and environmental change. Finally, we outline research questions that bridge the historically distinct fields of seasonal ecology and host-microbe interactions.

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Inter-individual variability in copepod microbiomes reveals bacterial networks linked to host physiology

Cited by 51 publications

References 53 publications

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

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

Meta-analysis cum machine learning approaches address the structure and biogeochemical potential of marine copepod associated bacteriobiomes

Animal-Microbe Interactions in the Context of Diapause

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