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Cited by 23Aquaculture disease management and microbiotaMicrobial Community Ecology and PhysiologyGut microbiota and health

Potential lineage transmission within the active microbiota of the eggs and the nauplii of the shrimp Litopenaeus stylirostris : possible influence of the rearing water and more

Open access
Giraud, Carolane, Callac, Nolwenn, Beauvais, Maxime, Mailliez, Jean-René, Ansquer, Dominique, Selmaoui-Folcher, Nazha, Pham, Dominique, Wabete, Nelly +1 more·2021·PeerJ
DOI 10.7717/peerj.12241PMC PMC8601056
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Abstract

Background: Microbial communities associated with animals are known to be key elements in the development of their hosts. In marine environments, these communities are largely under the influence of the surrounding water. In aquaculture, understanding the interactions existing between the microbiotas of farmed species and their rearing environment could help establish precise bacterial management. Method: In light of these facts, we studied the active microbial communities associated with the eggs and the nauplii of the Pacific blue shrimp ( Litopenaeus stylirostris ) and their rearing water. All samples were collected in September 2018, November 2018 and February 2019. After RNA extractions, two distinct Illumina HiSeq sequencings were performed. Due to different sequencing depths and in order to compare samples, data were normalized using the Count Per Million method. Results: We found a core microbiota made of taxa related to Aestuariibacter , Alteromonas , Vibrio , SAR11 , HIMB11 , AEGEAN 169 marine group and Candidatus Endobugula associated with all the samples indicating that these bacterial communities could be transferred from the water to the animals. We also highlighted specific bacterial taxa in the eggs and the nauplii affiliated to Pseudomonas , Corynebacterium , Acinetobacter , Labrenzia , Rothia , Thalassolituus , Marinobacter , Aureispira , Oleiphilus , Profundimonas and Marinobacterium genera suggesting a possible prokaryotic vertical transmission from the breeders to their offspring. This study is the first to focus on the active microbiota associated with early developmental stages of a farmed shrimp species and could serve as a basis to comprehend the microbial interactions involved throughout the whole rearing process.

AI snapshot

Written from the paper’s full text.

TL;DR

This study characterized the active bacterial communities associated with eggs, nauplii, and rearing water of farmed *Litopenaeus stylirostris* across three sampling periods. It found a shared core microbiota across all compartments and identified egg/nauplius-specific taxa absent from water, suggesting possible environmental acquisition plus potential vertical transmission from breeders.

Key findings

  • A total of 2,987,759 sequences clustered into 4,950 ASVs; 62 ASVs were shared among all water, egg, and nauplius samples, forming a core microbiota including *Aestuariibacter*, *Alteromonas*, *Vibrio*, SAR11, HIMB11, AEGEAN 169 marine group, and *Candidatus* Endobugula.
  • Water samples contained 257 unique ASVs, while 233 ASVs were found only in eggs and nauplii; eggs and nauplii shared 65 ASVs not detected in water, with egg-specific ASVs including *Pseudomonas* and *Corynebacterium* (each 18% relative abundance) and nauplius-specific ASVs including *Profundimonas* (15%) and *Marinobacterium* (8%).
  • In the shared core, *Aestuariibacter*, *Alteromonas*, and *Vibrio* represented over 50% of relative abundance in both eggs and nauplii, whereas primary reservoir samples were dominated (60%) by SAR11 Clade Ia, HIMB11, and an AEGEAN 169 marine group ASV.
  • CDOM absorption at 325 nm ranged from 0.8 to 1.1 m⁻¹; spectral slope ratios varied from 5.98 to 7.67 in primary reservoirs and 4.79 to 8.12 in secondary reservoirs.

Methods

  • Eggs, nauplii, and rearing water were sampled from the Ifremer Saint Vincent Bay hatchery in September 2018 (M1), November 2018 (M3), and February 2019 (M4); M4 eggs and nauplii were sampled in replicates, while M1 and M3 had unique egg and nauplius samples.
  • RNA was extracted, reverse-transcribed to cDNA, and the V4 region of the 16S rRNA gene was amplified and sequenced with Illumina HiSeq in two separate runs; data were normalized using Counts Per Million (CPM).
  • Sequences were processed with DADA2 to generate ASVs, taxonomy assigned using Silva 138, and community comparisons performed with Bray-Curtis dissimilarity, hierarchical clustering, and Venn diagrams.

Limitations

  • The paper states that vertical transmission could not be confirmed because several male breeders inseminate several females and eggs are pooled before larval rearing, making genealogy difficult to determine.
  • The paper notes that the effect of EDTA on active microbial communities in hatchery water is poorly known and requires further investigation, and that whether *Rothia* is part of the egg core microbiota or a contaminant remains unresolved.
  • Evident from the text: sample sizes were small, with unique egg/nauplius samples for M1 and M3 and replicates only for M4; two separate sequencing runs with different depths required normalization; and the study is descriptive/correlational, so proposed transmission routes are hypotheses rather than experimentally demonstrated.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.7717/peerj.12241

Cites

94 of 94 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 76 cited sources checked · 0 supported · 0 flagged

  • Findingreasoning

    The five genera Pseudomonas, Corynebacterium, Acinetobacter, Labrenzia and Rothia together represented more than 55% of total relative abundance among bacterial communities specifically associated with egg samples.

    “These five genera alone represented more than 55% of the total relative abundance among the bacterial communities specifically associated with the egg samples.”
    Quote in the paperNot a substantial claim
  • Findingown data

    All considered samples shared 62 ASVs.

    “All the considered samples shared 62 ASVs (Fig. 2B).”
    Quote in the paperSubstantial claim
  • Findingown data

    A total of 330 ASVs were shared among all primary reservoir samples.

    “A total of 330 ASVs were shared among all the primary reservoir samples (Fig. S2A).”
    Quote in the paperNot a substantial claim
  • Findingown data

    Among ASVs shared between eggs and nauplii, Thalassolituus was the most abundant genus at 20%.

    “The most abundant genera were Thalassolituus (20%), Vibrio (18%), Marinobacter (5%), Aureispira (5%) and Oleiphilus (4%).”
    Quote in the paperNot a substantial claim
  • Findingown data

    All water samples showed a large abundance of Gammaproteobacteria and Alphaproteobacteria.

    “Overall, all the water samples showed a large abundance of Gammaproteobacteria and Alphaproteobacteria (Fig. 1B)”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim. 45
  • May combine two claims. 28

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    In egg samples, Labrenzia and Rothia each accounted for 6% of total relative abundance.

    “Acinetobacter represented 8% of the total relative abundance while Labrenzia and Rothia each accounted for 6%.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    A total of 2,987,759 sequences were obtained from the Illumina sequencings of all samples.

    “A total of 2,987,759 sequences were obtained from the Illumina sequencings of all samples (M1, M3a, M3b and M4).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    SR values varied from 5.98 to 7.67 in the primary reservoirs and from 4.79 to 8.12 in the secondary reservoirs.

    “For all experiments, the SR values varied from 5.98 to 7.67 in the primary reservoirs (ResI) and from 4.79 to 8.12 in the secondary reservoirs (ResII).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The M3_ResII sample was dominated by Planctomycetes while the M4_ResII sample was mainly composed of Verrucomicrobiae.

    “The other water samples from the secondary reservoirs also contained Alphaproteobacteria and Gammaproteobacteria but Planctomycetes dominated the M3_ResII sample while the M4_ResII sample was mainly composed of Verrucomicrobiae.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In egg samples, Pseudomonas and Corynebacterium each had a relative abundance of 18%.

    “Pseudomonas and Corynebacterium each had a relative abundance of 18%.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    For the M1 experiment, the SR value was higher in the ResI sample (7.06) than in the ResII sample (4.79).

    “For the M1 experiment, the SR value was higher in the ResI sample (7.06) than in the ResII sample (4.79).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Hierarchical clustering based on Bray-Curtis similarity separated the samples into two distinct groups: cluster 1 contained all water samples and cluster 2 contained all egg and nauplius samples.

    “Hierarchical clustering based on Bray–Curtis similarity separated the samples into 2 distinct groups (Fig. 1A). The cluster 1 gathered all the water samples while the cluster 2 contained all the egg and the nauplius samples.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Eggs were also composed of Fusobacteriia, especially in the M1 experiment, while nauplii were partly composed of Desulfuromonadia.

    “Eggs were also composed of Fusobacteriia, especially for the M1 experiment, while nauplii were partly composed of Desulfuromonadia.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    For the M3 and M4 experiments, SR trends were inverted relative to M1, with SR values of 7.67 and 5.98 in the primary reservoirs and 8.12 and 6.27 in the secondary reservoirs.

    “For the M3 and the M4 experiments, trends were inverted (Table 1) as SR values respectively equaled 7.67 and 5.98 in the primary reservoirs; and 8.12 and 6.27 in the secondary reservoirs.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Sequences were clustered into 4,950 distinct ASVs.

    “Sequences were clustered into 4,950 distinct ASVs.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The M3 and M4 secondary reservoirs respectively displayed important abundances of Planctomycetes and Verrucomicrobiae.

    “The M3 and M4 secondary reservoirs respectively displayed important abundances of Planctomycetes and Verrucomicrobiae”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Gammaproteobacteria (45% of total ASV relative abundance) and Alphaproteobacteria (19%) were the most abundant classes, followed by Bacteroidia (10%) and Verrucomicrobiae (5%).

    “Gammaproteobacteria (45% of the total ASV relative abundance) and Alphaproteobacteria (19%) were the most abundant classes followed by Bacteroidia (10%) and Verrucomicrobiae (5%).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The a λ325 values of all reservoir samples ranged from 0.8 to 1.1 m−1.

    “The a λ325 values of all the reservoir samples ranged from 0.8 to 1.1 m−1.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Aesuariibacter, Alteromonas and Vibrio were present in all samples but dominated the eggs and nauplii.

    “Aesuariibacter, Alteromonas and Vibrio, which are ubiquitous genera in marine (Chan et al., 1978; Yi, Bae & Chun, 2004; Farmer et al., 2015), were present in all the samples but dominated the eggs and the nauplii (Figs. 4D and 4E).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    The microorganisms that were more represented in the water samples were completely different and belonged to very common marine groups (HIMB11, SAR11, AEGEAN).

    “Indeed, the microorganisms that were more represented in the water samples were completely different and belonged to very common marine groups (HIMB11, SAR11, AEGEAN) (Morris et al., 2002; Durham et al., 2014; Cram et al., 2015).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Morris et al., 2002 source

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    • cites Durham et al., 2014 source

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    • cites Cram et al., 2015 source

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  • May combine two claims.

    Findingcitation

    A total of 62 ASVs were shared among all compartments and were considered the core microbiota of all samples.

    “A total of 62 ASVs were shared among all compartments (Fig. 2B) and were considered to be the core microbiota of all our samples (Shade & Handelsman, 2012).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Shade & Handelsman, 2012

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  • May combine two claims.

    Findingown data

    Five genera (Vibrio, Marinobacter, Thalassotalea, Alteromonas and Aestuaribacter) were found in the ASVs shared between the eggs and the nauplii but also in the ASVs shared between the water reservoirs and the animals.

    “Interestingly, five genera (Vibrio, Marinobacter, Thalassotalea, Alteromonas and Aestuaribacter) were found in the ASVs shared between the eggs and the nauplii (Fig. 5C) but also in the ASVs shared between the water reservoirs and the animals (Fig. 4).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingcitation

    Aureispira bacteria were also abundant.

    “Aureispira bacteria were also abundant.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Planctomycetes and Verrucomicrobiae have been found in soil, freshwater and seawater.

    “which have been found in soil, freshwater (Australian dam, Hungarian pond) and seawater (the Californian Current) (Fuerst, 1995; Freitas et al., 2012).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Fuerst, 1995 source

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    • cites Freitas et al., 2012 source

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  • May combine two claims.

    Premisecitation

    Production of Litopenaeus stylirostris in New Caledonia has been declining due to seasonal vibriosis touching adult individuals and to larval mortalities that have not yet been explained.

    “Unfortunately, the production has been declining due to seasonal vibriosis touching adult individuals (Goarant et al., 1999; Goarant et al., 2006) and to larval mortalities that have not yet been explained.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Goarant et al., 1999 source

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    • cites Goarant et al., 2006 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Gammaproteobacteria and Alphaproteobacteria are respectively dominant classes in pelagic and benthic marine environments.

    “which are respectively dominant classes in pelagic and benthic marine environments (Zinger et al., 2011).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Zinger et al., 2011 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationcitation

    A change in CDOM measurements can result in a change of the microbiota and vice versa.

    “A change in the CDOM measurements can result in a change of the microbiota and vice versa.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Such SR-related changes occurred in the reservoirs and were of different natures during the M1 experiment compared to the M3 and M4 experiments.

    “suggesting that such changes occurred in the reservoirs and were of different natures during the M1 experiment compared to the M3 and M4 experiments.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Acidimicrobiia, Cyanobacteriia and Bacteroidia are classes previously identified in pelagic environments and marine ecosystems.

    “3 classes previously identified in pelagic environments and marine ecosystems (Giovannoni & Stingl, 2005; Zinger et al., 2011).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Giovannoni & Stingl, 2005

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    • cites Zinger et al., 2011 source

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    Interpretationreasoning

    Seasonal variations could explain the differences observed in the samples in terms of SR tendencies and differential bacterial communities.

    “As our samplings occurred between September 2018 and February 2019, seasonal variations could explain the differences observed in our samples in terms of SR tendencies and differential bacterial communities.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Shifts in SR can be correlated to molecular weight and composition modifications of dissolved organic matter.

    “Shifts in SR can be correlated to molecular weight and composition modifications of the dissolved organic matter (Helms et al., 2009)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Helms et al., 2009 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    CDOM measurements and bacterial compositions in water are known to be correlated factors.

    “CDOM measurements and bacterial compositions in water are known to be correlated factors (Judd, Crump & Kling, 2006).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Judd, Crump & Kling, 2006

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Pseudomonas, Acinetobacter and Labrenzia are genera found in marine environments.

    “Bacterial communities specifically associated with the egg samples (Fig. 5B) were dominated by Pseudomonas, Acinetobacter and Labrenzia, 3 genera found in marine environments (Fournier & Richet, 2006; Palleroni, 2015; Raj Sharma et al., 2019) and which had already been studied during the development of L. vannamei and P. monodon (Rungrassamee et al., 2013; Wang et al., 2020a; Wang et al., 2020b).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Fournier & Richet, 2006

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    • cites Palleroni, 2015 source

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    • cites Raj Sharma et al., 2019 source

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    Premisecitation

    Vibrios express genes involved in the metabolic degradation of chitin.

    “Vibrios are also known to express genes involved in the metabolic degradation of chitin (Hunt et al., 2008), an important component of the exoskeleton of the nauplii.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Hunt et al., 2008 source

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    Premisecitation

    Corynebacterium is a genus isolated from coral mucus.

    “The egg samples were also composed of Corynebacterium, a genera isolated from coral mucus (Ben-Dov et al., 2009).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Ben-Dov et al., 2009 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Gammaproteobacteria, Alphaproteobacteria and Bacteroidia have been identified in larvae of the Pacific white shrimp at early developmental stage and in intestines of adult black tiger shrimps.

    “These classes have been identified in larvae of the Pacific white shrimp (Litopenaeus vannamei) at early developmental stage (Pangastuti et al., 2009; Zheng et al., 2017) but also in the intestines of adult black tiger shrimps (Penaeus monodon) (Rungrassamee et al., 2013).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Pangastuti et al., 2009 source

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    • cites Zheng et al., 2017 source

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    • cites Rungrassamee et al., 2013 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    The total microbiota of the eggs and the nauplii may embrace the epibiota at the surface but also the endobiota.

    “As it has been shown for other animal species (brown trout, coho salmon), the total microbiota of the eggs and the nauplii may embrace the epibiota at the surface but also the endobiota (Nyholm, 2020).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Nyholm, 2020 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Rothia is considered as a sample contaminant in vent shrimps.

    “The eggs finally displayed large abundances of Rothia, usually found in human mouth cavities (Tsuzukibashi et al., 2017) and considered as sample contaminants in vent shrimps (Methou et al., 2019).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Methou et al., 2019 source

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  • May combine two claims.

    Interpretationreasoning

    These communities are present in the Saint Vincent Bay and persist throughout the reservoirs.

    “This could suggest that these communities are present in the Saint Vincent Bay and persist throughout the reservoirs.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Pseudomonas, Acinetobacter and Labrenzia had already been studied during the development of L. vannamei and P. monodon.

    “Bacterial communities specifically associated with the egg samples (Fig. 5B) were dominated by Pseudomonas, Acinetobacter and Labrenzia, 3 genera found in marine environments (Fournier & Richet, 2006; Palleroni, 2015; Raj Sharma et al., 2019) and which had already been studied during the development of L. vannamei and P. monodon (Rungrassamee et al., 2013; Wang et al., 2020a; Wang et al., 2020b).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Rungrassamee et al., 2013 source

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    • cites Wang et al., 2020a

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    • cites Wang et al., 2020b

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Candidatus Actinomarina, Synechococcus and SAR116 are ubiquitous in marine ecosystems and are known as or linked to primary producers.

    “These bacterial groups are ubiquitous in marine ecosystems and are known as or linked to primary producers (Britschgi & Giovannoni, 1991; Partensky & Vaulot, 1999; Ghai et al., 2013) .”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Britschgi & Giovannoni, 1991

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    • cites Partensky & Vaulot, 1999

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    • cites Ghai et al., 2013 source

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    Premisecitation

    UV treatment of rearing water induced selection of fast-growing and opportunistic bacteria.

    “This has already been noticed by Vadstein et al. who showed that UV treatment of rearing water induced selection of fast-growing and opportunistic bacteria (Vadstein et al., 2018).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Vadstein et al., 2018 source

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  • May combine two claims.

    Interpretationcitation

    Pseudomonas and Corynebacterium could find optimal growth conditions with shrimp eggs and the nauplii, explaining why they were so abundant among these samples.

    “Like Alteromonas and Vibrios, Pseudomonas and Corynebacterium are able to degrade different organic carbon sources using extracellular enzymes and could thus find optimal growth conditions with shrimp eggs and the nauplii explaining why they were so abundant among these samples (Palleroni, 2015; Tsuzukibashi et al., 2017).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Palleroni, 2015 source

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    • cites Tsuzukibashi et al., 2017 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Aesuariibacter, Alteromonas and Vibrio are ubiquitous genera in marine environments.

    “Aesuariibacter, Alteromonas and Vibrio, which are ubiquitous genera in marine (Chan et al., 1978; Yi, Bae & Chun, 2004; Farmer et al., 2015), were present in all the samples but dominated the eggs and the nauplii (Figs. 4D and 4E).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Chan et al., 1978 source

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    • cites Yi, Bae & Chun, 2004

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    • cites Farmer et al., 2015 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    OM60 Clade, Sva0996, MB11c04 and NS5 have been identified as crucial communities in the marine environment and found in various ecosystems ranging from marine sediments and surface seawaters to polar and coastal marine ecosystems.

    “They have been identified as crucial communities in the marine environment and have been found in various ecosystems ranging from marine sediments and surface seawaters to polar and coastal marine ecosystems (Suzuki et al., 2001; Cho et al., 2007; Gómez-Pereira et al., 2010; Orsi et al., 2016).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Suzuki et al., 2001 source

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    • cites Cho et al., 2007 source

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    • cites Gómez-Pereira et al., 2010 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Rothia is usually found in human mouth cavities.

    “The eggs finally displayed large abundances of Rothia, usually found in human mouth cavities (Tsuzukibashi et al., 2017) and considered as sample contaminants in vent shrimps (Methou et al., 2019).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Tsuzukibashi et al., 2017 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Bacteria affiliated to Alteromonas and Vibrio produce extracellular hydrolases involved in the biodegradation of various organic carbon sources.

    “Bacteria affiliated to Alteromonas and Vibrio produce extracellular hydrolases involved in the biodegradation of various organic carbon sources (Chan et al., 1978; Farmer et al., 2015).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Chan et al., 1978 source

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    • cites Farmer et al., 2015 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Vibrio and Oleiphilus have been identified in several marine environments and animals.

    “These communities were mainly composed of Vibrio and Oleiphilus which have been identified in several marine environments and animals (Golyshin et al., 2002; Farmer et al., 2015).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Golyshin et al., 2002 source

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    • cites Farmer et al., 2015 source

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  • Classified as probably not a substantial claim.

    Interpretationreasoning

    These ASVs could have been vertically transmitted as well as for the eggs.

    “These ASVs were specifically identified in the nauplius samples and could have been vertically transmitted as well as for the eggs.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    The microbiota associated to aquatic organisms and to their eggs are shaped by complex interactions between environmental and transmitted microorganisms.

    “This also shows that the microbiota associated to aquatic organisms and to their eggs are shaped by complex interactions between environmental and transmitted microorganisms (Sylvain & Derome, 2017).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Sylvain & Derome, 2017

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Marinobacterium have been highlighted in pipefish as a potential beneficial bacterium to larvae.

    “Marinobacterium have also been highlighted in pipefish as a potential beneficial bacterium to larvae (Beemelmanns et al., 2019) and some strains are also known to hydrolyse chitine suggesting that they could play an important role in growth at nauplius stage.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Beemelmanns et al., 2019 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    Marinobacterium could play an important role in growth at the nauplius stage.

    “Marinobacterium have also been highlighted in pipefish as a potential beneficial bacterium to larvae (Beemelmanns et al., 2019) and some strains are also known to hydrolyse chitine suggesting that they could play an important role in growth at nauplius stage.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Beemelmanns et al., 2019 source

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    • Rests on an assumption: Some strains of Marinobacterium are known to hydrolyse chitin.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Vertical transmission of 2 virus types has been proved using molecular techniques in the redclaw crayfish cultured in Australia.

    “Furthermore, a vertical transmission of 2 virus types has been proved using molecular techniques in the redclaw crayfish cultured in Australia (Jaroenram et al., 2021).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Jaroenram et al., 2021 source

      Not checked in the free run.

  • May combine two claims.

    Study design and conductreasoning

    The vertical transmission point has not yet been confirmed as several male breeders are used to inseminate several females which produce eggs that are pooled before larval rearing, making it difficult to determine the genealogy of the shrimps and their offspring.

    “This last point has not yet been confirmed as several male breeders are used to inseminate several females which produce eggs that are pooled before larval rearing, thus making it quite difficult to determine the genealogy of the shrimps and their offspring.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Aureispira have been isolated from marine sponges and algae and are thus frequently found in marine organisms.

    “They have been isolated from marine sponges and algae and are thus frequently found in marine organisms (Hosoya et al., 2006).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Hosoya et al., 2006 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Labrenzia are known to produce labrenzbactin, a catecholate-containing siderophore which demonstrates antimicrobial activity against Micrococcus luteus.

    “Concerning Labrenzia, they are known to produce labrenzbactin, a catecholate-containing siderophore which demonstrates an antimicrobial activity against Micrococcus luteus (Raj Sharma et al., 2019).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Raj Sharma et al., 2019 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Marinobacter and Thalassolituus have been isolated in farmed shrimp experiments.

    “Marinobacter and Thalassolituus have been isolated in farmed shrimp experiments (Dineshkumar et al., 2014).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Dineshkumar et al., 2014 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    There is a possible vertical transmission between the eggs and the nauplii and potentially from the breeders, as specific ASVs were not found in the rearing water.

    “As several ASVs were co-owned between the eggs and the nauplli, we also highlight a possible vertical transmission between the two compartments and potentially from the breeders as specific ASVs were not found in the rearing water (affiliated to Pseudomonas, Corynebacterium, Acinetobacter, Labrenzia, Rothia, Thalassolituus, Marinobacter, Aureispira, Oleiphilus, Profundimonas, Marinobacterium) (Fig”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Marinobacter and Aestuariibacter have been identified in the rearing environment of adult L. vannamei and brackishwater shrimps.

    “Marinobacter and Aestuariibacter have been identified in the rearing environment of adult L. vannamei and brackishwater shrimps (Chen et al., 2019; Dineshkumar et al., 2014).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Chen et al., 2019 source

      Not checked in the free run.

    • cites Dineshkumar et al., 2014 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Vertical transmission has been suggested in hydrothermal shrimps where the eggs were associated with specific bacterial communities that were not found in the environment.

    “Vertical transmission has also been suggested in hydrothermal shrimps where the eggs were associated with specific bacterial communities that were not found in the environment (Methou et al., 2019).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Methou et al., 2019 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    The nauplius samples could also be under the influence of bacterial communities associated with the eggs as specific ASVs seemed to be transmitted between the 2 sample types.

    “The nauplius samples could also be under the influence of bacterial communities associated with the eggs as specific ASVs seemed to be transmitted between the 2 sample types (Fig. 5C).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Vibrio have been identified in adults and nauplii of L. vannamei shrimps regardless of their health status.

    “Even though Vibrio sp. can be associated with diseases, they have been identified in adults and nauplii of L. vannamei shrimps regardless of their health status (Vandenberghe et al., 1999; Cornejo-Granados et al., 2017).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Vandenberghe et al., 1999 source

      Not checked in the free run.

    • cites Cornejo-Granados et al., 2017 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Thalassolituus has been identified at the nauplius stage of L. vannamei and has been suggested as a beneficial bacterium for larval development.

    “Thalassolituus has also been identified at the nauplius stage of L. vannamei and has been suggested as a beneficial bacterium for larval development (Wang et al., 2020a; Wang et al., 2020b).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Wang et al., 2020a

      Not checked in the free run.

    • cites Wang et al., 2020b

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Profundimonas and Marinobacterium are both aerobic Gammaproteobacteria isolated from seawater samples.

    “The most abundant genera were Profundimonas and Marinobacterium which are both aerobic Gammaproteobacteria isolated from seawater samples (González et al., 1997; Cao et al., 2014).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites González et al., 1997 source

      Not checked in the free run.

    • cites Cao et al., 2014 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Vibrio, Alteromonas and Thalassotalea have all been spotted in L. vannamei at different developmental stages as well as in the surrounding water.

    “Vibrio, Alteromonas and Thalassotalea have all been spotted in L. vannamei at different developmental stages as well as in the surrounding water (Wang et al., 2020a; Wang et al., 2020b; Zhang et al., 2014; Zheng et al., 2017).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Wang et al., 2020a

      Not checked in the free run.

    • cites Wang et al., 2020b

      Not checked in the free run.

    • cites Zhang et al., 2014 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Intraovum vertical transmission has been highlighted in farmed fish eggs, accounting for 20% of the total bacterial relative abundance in eggs.

    “Intraovum vertical transmission has already been highlighted in farmed fish eggs, accounting for 20% of the total bacterial relative abundance in eggs (Hansen & Olafsen, 1999).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Hansen & Olafsen, 1999

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Some species are known to be selected in the environment by their host as symbionts.

    “Some species are even known to be selected in the environment by their host as symbionts (Nyholm & McFall-Ngai, 2004).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Nyholm & McFall-Ngai, 2004

      Not checked in the free run.

62 of 62

  • The paper relies on this without support.

    Shared ASVs between water and animal samples reflect transfer or colonization from the rearing water rather than independent occurrence or contamination.

    “indicating that these bacterial communities could be transferred from the water to the animals”
    “suggesting that some bacterial communities in the rearing environment could potentially colonize the eggs and the nauplii”

  • The paper relies on this without support.

    Specific taxa found in eggs and nauplii but not in water samples were not acquired from water or other environmental sources; their absence in water samples indicates absence in the water environment.

    “We also found specific taxa related to Pseudomonas, Corynebacterium, Acinetobacter, Labrenzia, Rothia, Thalassolituus, Marinobacter, Aureispira, Oleiphilus, Profundimonas and Marinobacterium genera in the eggs and the nauplii that were not found in the water samples and could have been vertically transmitted from the breeders.”

  • The paper relies on this without support.

    The New Caledonian lagoon has been increasingly exposed to anthropic pressures over the years.

    “the New Caledonian lagoon has been more and more exposed to anthropic pressures over the years”

  • The paper relies on this without support.

    This study is the first to focus on the active microbiota of the eggs and the nauplii of a farmed shrimp species while considering the impact of the rearing water.

    “To our knowledge, this study is the first to focus on the active microbiota of the eggs and the nauplii of a farmed shrimp species while considering the impact of the rearing water.”

  • The paper relies on this without support.

    Some strains of Marinobacterium are known to hydrolyse chitin.

    “Marinobacterium have also been highlighted in pipefish as a potential beneficial bacterium to larvae (Beemelmanns et al., 2019) and some strains are also known to hydrolyse chitine suggesting that they could play an important role in growth at nauplius stage.”

  • The paper relies on this without support.

    Vibrio sp. can be associated with diseases.

    “Even though Vibrio sp. can be associated with diseases, they have been identified in adults and nauplii of L. vannamei shrimps regardless of their health status (Vandenberghe et al., 1999; Cornejo-Granados et al., 2017).”
6 of 6

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • These three major bacterial classes had been previously identified in water samples collected from the water reservoirs of the Saint Vincent experimental shrimp hatchery in October and November 2018 and February 2019.

    “These three major bacterial classes had been previously identified in water samples collected from the water reservoirs of the Saint Vincent experimental shrimp hatchery in October and November 2018 and February 2019.”

    From The Active Microbiota of the Eggs and the Nauplii of the Pacific Blue Shrimp Litopenaeus stylirostris Partially Shaped by a Potential Vertical Transmission (2022) · cites this paper as Giraud et al., 2021

    The Results (Microbial diversity) identify major bacterial classes in the reservoir water samples, including Alphaproteobacteria, Gammaproteobacteria and Bacteroidia. The Materials & Methods (Study design and sample collection) place the experiments in September 2018, November 2018 and February 2019—not October 2018 as claimed. (LLM, conf=0.90)

    Experimental — accuracy not yet measured

  • In a previous study, several bacterial families were specifically associated with the eggs and the nauplii of L. stylirostris and were not found in the environment, leading to the hypothesis that they had been acquired from the breeders.

    “Indeed, studying the active microbiota associated with the early larval stages (eggs and nauplii) of L. stylirostris as well as with their rearing environment, several bacterial families were specifically associated with the eggs and the nauplii and were not found in the environment leading us to hypothesize that they had been acquired from the breeders.”

    From The Active Microbiota of the Eggs and the Nauplii of the Pacific Blue Shrimp Litopenaeus stylirostris Partially Shaped by a Potential Vertical Transmission (2022) · cites this paper as Giraud et al., 2021

    The Introduction (page not available) reports taxa associated with eggs and nauplii that were absent from rearing-water samples and could have been transmitted from breeders. The paper identifies those taxa by genus, however, not as bacterial families specifically absent from the environment. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Vibrionaceae, Rhodobacteraceae, Flavobacteriaceae, Pseudoalteromonadaceae, Oceanospirillaceae, Colwelliaceae, and Alteromonadaceae have been found in larvae and adults of different shrimp species.

    “Thus, Vibrionaceae, Rhodobacteraceae, Flavobacteriaceae, Pseudoalteromonadaceae, Oceanospirillaceae, Colwelliaceae, and Alteromonadaceae were found in larvae and adults of different shrimp species.”

    From The Active Microbiota of the Eggs and the Nauplii of the Pacific Blue Shrimp Litopenaeus stylirostris Partially Shaped by a Potential Vertical Transmission (2022) · cites this paper as Giraud et al., 2021

    The Discussion (page unavailable) reports Vibrio and Alteromonas in shrimp eggs and nauplii and describes their detection at other developmental stages, including adults. It does not establish the claim for all seven named families in larvae and adults of different shrimp species; the paper chiefly reports classes and genera rather than that family-level list. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • Some bacterial lineages associated with the early larval stages of the Pacific blue shrimp Litopenaeus stylirostris could be acquired from the breeders via a potential vertical transmission.

    “In a previous article, we have concluded that some bacterial lineages associated with the early larval stages of the Pacific blue shrimp Litopenaeus stylirostris could be acquired from the breeders via a potential vertical transmission.”

    From The Active Microbiota of the Eggs and the Nauplii of the Pacific Blue Shrimp Litopenaeus stylirostris Partially Shaped by a Potential Vertical Transmission (2022) · cites this paper as Giraud et al., 2021

  • Reservoir samples also showed high abundances of Acidimicrobiia, Cyanobacteriia, and Planctomycetes.

    “However, these reservoir samples also showed high abundances of Acidimicrobiia, Cyanobacteriia, and Planctomycetes (Giraud et al., 2021).”

    From The Active Microbiota of the Eggs and the Nauplii of the Pacific Blue Shrimp Litopenaeus stylirostris Partially Shaped by a Potential Vertical Transmission (2022) · cites this paper as Giraud et al., 2021

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Conflicting counts of ASVs unique to nauplii

    Minor

    The results report 80 ASVs unique to nauplius samples, while the Figure 5 caption reports 88.

  • Conflicting counts of ASVs unique to primary reservoirs

    Minor

    The results report 145 ASVs specific to the primary reservoirs, but the Figure 3 caption reports 148 for the same subset.

2 of 2

Cites

Flagged first, then by citations

Research works printed but not linked: 3

  1. Beliaeff, 2009, DEDUCTION: a research project for shrimp farming sustainability in New Caledonia
  2. Harrison, 1997, Broodstock nutrition and maturation diets, 390
  3. Partensky, 1999, Cyanobacterial photosynthetic apparatus: an overview, Marine Cyanobacteria, 19, 457

Cited by

Sorted by citations

Related

Authors
Giraud, C., Callac, N., Beauvais, M., Mailliez, J.-R., Ansquer, D., Selmaoui-Folcher, N., Pham, D., Wabete, N., & Boulo, V.
Affiliations
  • University of New Caledonia (NC)
  • University of New Caledonia, Institut des Sciences Exactes et Appliquées (ISEA), Noumea, New Caledonia
Corresponding author
  • Giraud, Carolane
  • Callac, Nolwenn
ORCID
Venue
PeerJ
Publisher
PeerJ
Published
2021-11-15
Volume
9
Pages
e12241
ISSN
2167-8359 (ISSN-L)
DOI
10.7717/peerj.12241
PMC
PMC8601056
OpenAlex
W3214184732
Semantic Scholar
fb65b6c2b5cb2bfefa6bea77c63e0234a466b963
Cited by
23
References
94
Citations by year
2025: 6 · 2024: 3 · 2023: 11 · 2022: 3
FWCI
1.59
Type
journal article
Language
en
Open access
Licence
Locations
  • PeerJ (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, other-oa)
  • Institutional Archive of Ifremer (French Research Institute for Exploitation of the Sea) (submittedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
The RESSAC project (LEAD-NC, Ifremer New-Caledonia) within the framework agreement with the New Caledonian Provinces and Government and by the Pacific Doctoral School
Topics
  • Life Sciences › Immunology and Microbiology › Immunology › Aquaculture disease management and microbiota
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords
Litopenaeus stylirostris, shrimp eggs, nauplii, vertical transmission, core microbiome, bacterial community composition, early developmental stages, aquaculture, Alteromonas, Vibrio, Pseudomonas

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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-10.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-10.

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