scholarly journals Metabarcoding littoral hard-bottom communities: unexpected diversity and database gaps revealed by two molecular markers

2017 ◽  
Author(s):  
Owen S Wangensteen ◽  
Creu Palacín ◽  
Magdalena Guardiola ◽  
Xavier Turon
Keyword(s):  
Molecular Markers ◽  
National Parks ◽  
Benthic Communities ◽  
Taxonomic Resolution ◽  
Universal Primers ◽  
Taxonomic Assignment ◽  
Identification Rate ◽  
Bottom Communities ◽  
Reference Databases ◽  
Hard Bottom Communities

We developed a metabarcoding method for biodiversity characterization of structurally complex natural marine hard-bottom communities. Novel primer sets for two different molecular markers: the “Leray fragment” of mitochondrial cytochrome c oxidase, COI, and the V7 region of ribosomal RNA 18S were used to analyse eight different marine shallow benthic communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea). Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. We found unexpectedly high values for MOTU richness, suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignation of the detected sequences. Nevertheless, over 90% (in abundance) of the sequenced reads could be successfully assigned to phylum or lower taxonomical level. This identification rate might be significantly improved in the future, as reference databases are updated. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples, and emerges as a robust, fast, objective and affordable method for comprehensively characterizing the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans, allowing for standardized biomonitoring of these ecologically important communities. The new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities.

scholarly journals Metabarcoding littoral hard-bottom communities: unexpected diversity and database gaps revealed by two molecular markers

2017 ◽  
Author(s):  
Owen S Wangensteen ◽  
Creu Palacín ◽  
Magdalena Guardiola ◽  
Xavier Turon
Keyword(s):  
Molecular Markers ◽  
National Parks ◽  
Benthic Communities ◽  
Taxonomic Resolution ◽  
Universal Primers ◽  
Taxonomic Assignment ◽  
Identification Rate ◽  
Bottom Communities ◽  
Reference Databases ◽  
Hard Bottom Communities

We developed a metabarcoding method for biodiversity characterization of structurally complex natural marine hard-bottom communities. Novel primer sets for two different molecular markers: the “Leray fragment” of mitochondrial cytochrome c oxidase, COI, and the V7 region of ribosomal RNA 18S were used to analyse eight different marine shallow benthic communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea). Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. We found unexpectedly high values for MOTU richness, suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignation of the detected sequences. Nevertheless, over 90% (in abundance) of the sequenced reads could be successfully assigned to phylum or lower taxonomical level. This identification rate might be significantly improved in the future, as reference databases are updated. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples, and emerges as a robust, fast, objective and affordable method for comprehensively characterizing the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans, allowing for standardized biomonitoring of these ecologically important communities. The new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities.

scholarly journals DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4705 ◽  
Author(s):  
Owen S. Wangensteen ◽  
Creu Palacín ◽  
Magdalena Guardiola ◽  
Xavier Turon
Keyword(s):  
Molecular Markers ◽  
Taxonomic Resolution ◽  
Universal Primers ◽  
Biodiversity Assessment ◽  
Taxonomic Assignment ◽  
Bottom Communities ◽  
Dna Metabarcoding ◽  
Reference Databases ◽  
Hard Bottom Communities ◽  
High Diversity

Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular markers: the “Leray fragment” of mitochondrialcytochrome c oxidase(COI), for which a novel primer set was developed, and the V7 region of the nuclear small subunit ribosomal RNA (18S). Eight different shallow marine littoral communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea) were studied. Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. Despite applying stringent filters, we found high values for MOTU richness (2,510 and 9,679 MOTUs with 18S and COI, respectively), suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignment of the detected sequences. In our dataset, 85% of 18S MOTUs and 64% of COI MOTUs could be identified to phylum or lower taxonomic level. Nevertheless, those unassigned were mostly rare MOTUs with low numbers of reads, and assigned MOTUs comprised over 90% of the total sequence reads. The identification rate might be significantly improved in the future, as reference databases are further completed. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples. Thus, eukaryotic metabarcoding emerges as a robust, fast, objective and affordable method to comprehensively characterize the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans. The 18S marker lacks species-level resolution and thus cannot be recommended to assess the detailed taxonomic composition of these communities. Our new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities.

Regionalization of benthic hard-bottom communities across the Pourtalès Terrace, Florida

2021 ◽  
Vol 172 ◽  
pp. 103514
Author(s):  
Brian K. Walker ◽  
Charles Messing ◽  
Jana Ash ◽  
Sandra Brooke ◽  
John K. Reed ◽  
...  
Keyword(s):  
Bottom Communities ◽  
Hard Bottom Communities

Succession and seasonal onset of colonization in subtidal hard-bottom communities off northern Chile

2010 ◽  
Vol 32 (1) ◽  
pp. 75-87 ◽  
Author(s):  
Aldo S. Pacheco ◽  
Jürgen Laudien ◽  
Martin Thiel ◽  
Marcelo Oliva ◽  
Olaf Heilmayer
Keyword(s):  
Northern Chile ◽  
Bottom Communities ◽  
Hard Bottom Communities

scholarly journals Effects of climate and eutrophication on the diversity of hard bottom communities on the Skagerrak coast 1990-2010

2015 ◽  
Vol 530 ◽  
pp. 29-46 ◽  
Author(s):  
KM Norderhaug ◽  
H Gundersen ◽  
A Pedersen ◽  
F Moy ◽  
N Green ◽  
...  
Keyword(s):  
Bottom Communities ◽  
Hard Bottom Communities

scholarly journals In situ filamentous communities from the Ediacaran (approx. 563 Ma) of Brazil

2021 ◽  
Vol 288 (1942) ◽  
pp. 20202618
Author(s):  
Bruno Becker-Kerber ◽  
Gabriel Eduardo Baréa de Barros ◽  
Paulo Sergio Gomes Paim ◽  
Gustavo M. E. M. Prado ◽  
Ana Lucia Zucatti da Rosa ◽  
...  
Keyword(s):  
Oxygen Concentration ◽  
Benthic Communities ◽  
Preferred Orientation ◽  
Redox Condition ◽  
Taxonomic Assignment ◽  
Diagnostic Features ◽  
Ecological Dynamics ◽  
Widespread Occurrence ◽  
Biological Affinity

Precambrian filamentous microfossils are common and diverse. Nevertheless, their taxonomic assignment can be difficult owing to their overall simple shapes typically lacking in diagnostic features. Here, we report in situ communities of well-preserved, large filamentous impressions from the Ediacaran Itajaí Basin ( ca 563 Ma) of Brazil. The filaments are uniserial (unbranched) and can reach up to 200 µm in width and up to 44 mm in length. They occur as both densely packed or sparsely populated surfaces, and typically show a consistent orientation. Although simple in shape, their preferred orientation suggests they were tethered to the seafloor, and their overall flexibility (e.g. bent, folded and twisted) supports a biological (rather than sedimentary) affinity. Biometric comparisons with modern filamentous groups further support their biological affinity, suggesting links with either large sulfide-oxidizing bacteria (SOB) or eukaryotes. Other morphological and palaeoecological characteristics further corroborates their similarities with modern large filamentous SOB. Their widespread occurrence and association with complex Ediacaran macrobiota (e.g. frondose organisms, Palaeopascichnus ) suggest that they probably played an important role in the ecological dynamics of these early benthic communities by providing firm substrates for metazoans to inhabit. It is further hypothesized that the dynamic redox condition in the latest Ediacaran, with the non-continuous rise in oxygen concentration and periods of hypoxia, may have created ideal conditions for SOB to thrive.

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