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Research article
Diversity and distribution of marine heterotrophic bacteria from a large culture collection
Silvia G. Acinas
Consejo Superior de Investigaciones Cientificas
Corresponding Author
ORCiD: https://orcid.org/0000-0002-3439-0428
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Microbiology.
Background: Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. We described the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along different depths.
Results: The partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing all photic, mesopelagic, and bathypelagic isolates sequences retrieved from different stations, 37% of them were 100% identical. This percentage increased up to 59% when mesopelagic and bathypelagic strains were grouped as the aphotic dataset and compared to the photic dataset of isolates, indicating the ubiquity of some bacterial isolates along different ocean depths. Finally, we isolated three strains that represent a new species, and the genome comparison and phenotypic characterization of two of these strains (ISS653 and ISS1889) concluded that they belong to a new species within the genus Mesonia.
Conclusions: Overall, this study highlights the relevance of culture-dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of the culturable marine bacteria as part of the total marine microbial diversity.
Keywords
bacterial isolates, deep ocean, photic ocean, diversity
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CURRENT STATUS: Published
Version 2
Posted 09 Jun, 2020
Published
On 13 Jul, 2020
No community comments so far
Editorial decision: Accept
On 26 Jun, 2020
Review #1 received
Received 25 Jun, 2020
Review #2 received
Received 15 Jun, 2020
Reviewer #2 agreed
On 13 Jun, 2020
Reviewer #1 agreed
On 10 Jun, 2020
Reviewers invited
Invitations sent on 08 Jun, 2020
Editor assigned
On 03 Jun, 2020
Submission checks complete
On 02 Jun, 2020
Editor invited
On 02 Jun, 2020
No comments provided
Editorial decision: Major revision
On 22 Apr, 2020
Review #2 received
Received 09 Apr, 2020
Review #1 received
Received 03 Apr, 2020
Reviewers invited
Invitations sent on 18 Mar, 2020
Reviewer #1 agreed
On 18 Mar, 2020
Reviewer #2 agreed
On 18 Mar, 2020
Reviewer #3 agreed
On 18 Mar, 2020
Submission checks complete
On 11 Mar, 2020
Editor invited
On 11 Mar, 2020
Editor assigned
On 05 Mar, 2020
First submitted
On 03 Mar, 2020
Metrics
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PDF Downloads: ...
HTML Views: ...
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This preprint is under consideration at BMC Microbiology. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Diversity and distribution of marine heterotrophic bacteria from a large culture collection
Silvia G. Acinas
Consejo Superior de Investigaciones Cientificas
Corresponding Author
ORCiD: https://orcid.org/0000-0002-3439-0428
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 2
Posted 09 Jun, 2020
Published
On 13 Jul, 2020
No community comments so far
Editorial decision: Accept
On 26 Jun, 2020
Review #1 received
Received 25 Jun, 2020
Review #2 received
Received 15 Jun, 2020
Reviewer #2 agreed
On 13 Jun, 2020
Reviewer #1 agreed
On 10 Jun, 2020
Reviewers invited
Invitations sent on 08 Jun, 2020
Editor assigned
On 03 Jun, 2020
Submission checks complete
On 02 Jun, 2020
Editor invited
On 02 Jun, 2020
No comments provided
Editorial decision: Major revision
On 22 Apr, 2020
Review #2 received
Received 09 Apr, 2020
Review #1 received
Received 03 Apr, 2020
Reviewers invited
Invitations sent on 18 Mar, 2020
Reviewer #1 agreed
On 18 Mar, 2020
Reviewer #2 agreed
On 18 Mar, 2020
Reviewer #3 agreed
On 18 Mar, 2020
Submission checks complete
On 11 Mar, 2020
Editor invited
On 11 Mar, 2020
Editor assigned
On 05 Mar, 2020
First submitted
On 03 Mar, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Microbiology.
Background: Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. We described the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along different depths.
Results: The partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing all photic, mesopelagic, and bathypelagic isolates sequences retrieved from different stations, 37% of them were 100% identical. This percentage increased up to 59% when mesopelagic and bathypelagic strains were grouped as the aphotic dataset and compared to the photic dataset of isolates, indicating the ubiquity of some bacterial isolates along different ocean depths. Finally, we isolated three strains that represent a new species, and the genome comparison and phenotypic characterization of two of these strains (ISS653 and ISS1889) concluded that they belong to a new species within the genus Mesonia.
Conclusions: Overall, this study highlights the relevance of culture-dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of the culturable marine bacteria as part of the total marine microbial diversity.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5