scholarly journals A universal subcuticular bacterial symbiont of a coral predator, the crown-of-thorns starfish, in the Indo-Pacific

2020 ◽  
Author(s):  
Naohisa Wada ◽  
Hideaki Yuasa ◽  
Rei Kajitani ◽  
Yasuhiro Gotoh ◽  
Yoshitoshi Ogura ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
16S Rrna ◽  
Marine Invertebrates ◽  
Sequence Data ◽  
The Body ◽  
Rrna Gene ◽  
Ecological Knowledge ◽  
Reef Management ◽  
Genetic Traits ◽  
Associated Bacteria

AbstractBackgroundPopulation outbreaks of the crown-of-thorns starfish (Acanthaster planci sensu lato; COTS), a primary predator of reef-building corals in the Indo-Pacific Ocean, are major concerns in coral reef management. While biological and ecological knowledge of COTS has been accumulating since the 1960s, little is known about its associated bacteria. The aim of this study was to provide fundamental information on dominant COTS-associated bacteria through a multifaceted molecular approach.MethodsA total of 205 COTS individuals from 17 locations throughout the Indo-Pacific Ocean were examined for the presence of COTS-associated bacteria. We conducted 16S rRNA metabarcoding of COTS to determine the bacterial profiles of different parts of the body, and generated a full-length 16S rRNA gene sequence from a single dominant bacterium, which we designated COTS27. We performed phylogenetic analysis to determine the taxonomy, screening of COTS27 across the Indo-Pacific, FISH to visualize it within the COTS tissues, and reconstruction of the chromosome from the hologenome sequence data.ResultsWe discovered that a single bacterium exists at high densities in the subcuticular space in COTS forming a biofilm-like structure between the cuticle and the epidermis. COTS27 belongs to a clade that presumably represents a distinct order (so-called marine spirochetes) in the phylum Spirochaetes and is universally present in COTS throughout the Indo-Pacific Ocean. The reconstructed genome of COTS27 includes some genetic traits that are probably linked to adaptation to marine environments and evolution as an extracellular endosymbiont in subcuticular spaces.ConclusionsCOTS27 can be found in three allopatrically speciated COTS species, ranging from northern Red Sea to the Pacific, implying that symbiotic relationship arose before the speciation (approximately 2 million years ago). The universal association of COTS27 with COTS and nearly mono-specific association at least with the Indo-Pacific COTS potentially provides a useful model system for studying symbiont-host interactions in marine invertebrates.

scholarly journals Molecular Characterization of Sub-cuticular Bacteria in New Zealand Echinoderms

2021 ◽  
Author(s):  
◽  
Scott Anthony Lawrence
Keyword(s):  
Phylogenetic Analysis ◽  
New Zealand ◽  
16S Rrna ◽  
Culture Media ◽  
Molecular Techniques ◽  
The Body ◽  
Rrna Gene ◽  
Associated Bacteria ◽  
The Relationship

<p>Many echinoderms contain sub-cuticular bacteria (SCB), symbionts which reside in the lumen between the epidermal cells and the outer cuticle of the host. The relationship is very common, with ~60% of all echinoderms studied so far containing SCB. Currently, little is known about the function of the symbiosis, although it has been hypothesized that SCB may aid in host nutrition or antimicrobial defense. Whatever their function, the large numbers of SCB observed in many echinoderms (10 (to the power of 8) - 10 (to the power of 9) SCB g-1 AFDW host tissue) suggest that they may be important to the host. Factors contributing to the lack of knowledge about the echinoderm-SCB symbiosis include the difficulty associated with cultivating symbiotic bacteria, and the lack of studies identifying the SCB by molecular means. In this study, molecular techniques were employed to characterize the SCB of several common New Zealand echinoderms. The specific objectives of the study were to identify the SCB through sequencing of a region of the bacterial 16S rRNA gene, identify and locate SCB in situ through the use of fluorescence in situ hybridization (FISH), and cultivate SCB obtained from those echinoderms which were found to contain them. Phylogenetic analysis of 16S rRNA sequences obtained from echinoderm-associated bacteria resulted in the identification of four putative species of SCB. All four bacteria were isolated from samples of Stichopus mollis (class Holothuroidea), and two of the four were also found in samples of Patiriella sp (class Asteroidea). The first putative SCB belongs to the order Rhizobiales (a-proteobacteria), and is closely related to the SCB previously isolated from the brittle star Ophiactis balli. The second species belongs to the order Chromatiales (y-proteobacteria). Putative SCB species 3 falls within the Roseobacter clade (a-proteobacteria). The phylogenetic placement of the final putative SCB is more ambiguous, as this bacterium falls among members of the a- and y- subdivisions of the phylum Proteobacteria. The nearest relatives of this final bacterium are in the orders Rickettsiales and Thiotrichales. Results of FISH assays show that Patiriella sp. and S. mollis contain SCB, while a third species, Astrostole scabra (class Asteroidea) does not. The SCB community composition was found to vary between Patiriella sp. and S. mollis. In both species, the majority of the SCB present were found to belong to the a-subdivision of the phylum Proteobacteria (>80% in both species). However, in S. mollis, ~20% of the SCB community consists of bacteria belonging to the y-subdivision of the phylum Proteobacteria, whereas bacteria belonging to this subdivision were never observed in Patiriella sp. Cultivation experiments were carried out using a range of culture media, however results were inconclusive. Ten species of proteobacteria were successfully cultivated, three of which were obtained only from Patiriella sp. and S. mollis samples and were considered possible candidates for SCB. However, phylogenetic analysis of these three bacteria revealed that closely-related bacteria are predominantly free-living species. While the possibility remains that these three bacteria are in fact SCB, it seems more likely that they represent seawater or echinoderm surface-associated bacteria. This study contributes to the body of knowledge of the echinoderm-SCB symbiosis by identifying several potential SCB in Patiriella sp. and S. mollis, and is the first to identify SCB in situ through the use of FISH. An obvious goal in studies of the echinoderm-SCB symbiosis is to determine the function of the relationship. Potential functions of the symbiosis, based on the results obtained here, are discussed herein.</p>

scholarly journals Molecular Characterization of Sub-cuticular Bacteria in New Zealand Echinoderms

2021 ◽  
Author(s):  
◽  
Scott Anthony Lawrence
Keyword(s):  
Phylogenetic Analysis ◽  
New Zealand ◽  
16S Rrna ◽  
Culture Media ◽  
Molecular Techniques ◽  
The Body ◽  
Rrna Gene ◽  
Associated Bacteria ◽  
The Relationship

<p>Many echinoderms contain sub-cuticular bacteria (SCB), symbionts which reside in the lumen between the epidermal cells and the outer cuticle of the host. The relationship is very common, with ~60% of all echinoderms studied so far containing SCB. Currently, little is known about the function of the symbiosis, although it has been hypothesized that SCB may aid in host nutrition or antimicrobial defense. Whatever their function, the large numbers of SCB observed in many echinoderms (10 (to the power of 8) - 10 (to the power of 9) SCB g-1 AFDW host tissue) suggest that they may be important to the host. Factors contributing to the lack of knowledge about the echinoderm-SCB symbiosis include the difficulty associated with cultivating symbiotic bacteria, and the lack of studies identifying the SCB by molecular means. In this study, molecular techniques were employed to characterize the SCB of several common New Zealand echinoderms. The specific objectives of the study were to identify the SCB through sequencing of a region of the bacterial 16S rRNA gene, identify and locate SCB in situ through the use of fluorescence in situ hybridization (FISH), and cultivate SCB obtained from those echinoderms which were found to contain them. Phylogenetic analysis of 16S rRNA sequences obtained from echinoderm-associated bacteria resulted in the identification of four putative species of SCB. All four bacteria were isolated from samples of Stichopus mollis (class Holothuroidea), and two of the four were also found in samples of Patiriella sp (class Asteroidea). The first putative SCB belongs to the order Rhizobiales (a-proteobacteria), and is closely related to the SCB previously isolated from the brittle star Ophiactis balli. The second species belongs to the order Chromatiales (y-proteobacteria). Putative SCB species 3 falls within the Roseobacter clade (a-proteobacteria). The phylogenetic placement of the final putative SCB is more ambiguous, as this bacterium falls among members of the a- and y- subdivisions of the phylum Proteobacteria. The nearest relatives of this final bacterium are in the orders Rickettsiales and Thiotrichales. Results of FISH assays show that Patiriella sp. and S. mollis contain SCB, while a third species, Astrostole scabra (class Asteroidea) does not. The SCB community composition was found to vary between Patiriella sp. and S. mollis. In both species, the majority of the SCB present were found to belong to the a-subdivision of the phylum Proteobacteria (>80% in both species). However, in S. mollis, ~20% of the SCB community consists of bacteria belonging to the y-subdivision of the phylum Proteobacteria, whereas bacteria belonging to this subdivision were never observed in Patiriella sp. Cultivation experiments were carried out using a range of culture media, however results were inconclusive. Ten species of proteobacteria were successfully cultivated, three of which were obtained only from Patiriella sp. and S. mollis samples and were considered possible candidates for SCB. However, phylogenetic analysis of these three bacteria revealed that closely-related bacteria are predominantly free-living species. While the possibility remains that these three bacteria are in fact SCB, it seems more likely that they represent seawater or echinoderm surface-associated bacteria. This study contributes to the body of knowledge of the echinoderm-SCB symbiosis by identifying several potential SCB in Patiriella sp. and S. mollis, and is the first to identify SCB in situ through the use of FISH. An obvious goal in studies of the echinoderm-SCB symbiosis is to determine the function of the relationship. Potential functions of the symbiosis, based on the results obtained here, are discussed herein.</p>

scholarly journals Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

2009 ◽  
Vol 75 (23) ◽  
pp. 7537-7541 ◽  
Author(s):  
Patrick D. Schloss ◽  
Sarah L. Westcott ◽  
Thomas Ryabin ◽  
Justine R. Hall ◽  
Martin Hartmann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Software Package ◽  
Sequence Data ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Laptop Computer ◽  
Operational Taxonomic Units ◽  
Β Diversity ◽  
Single Piece

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

scholarly journals Sponge-Associated Bacteria Are Strictly Maintained in Two Closely Related but Geographically Distant Sponge Hosts

2011 ◽  
Vol 77 (20) ◽  
pp. 7207-7216 ◽  
Author(s):  
Naomi F. Montalvo ◽  
Russell T. Hill
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Sponge Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Associated Bacteria ◽  
Content Type ◽  
Key Species ◽  
Sponge Associated Bacteria

ABSTRACTThe giant barrel spongesXestospongiamutaandXestospongiatestudinariaare ubiquitous in tropical reefs of the Atlantic and Pacific Oceans, respectively. They are key species in their respective environments and are hosts to diverse assemblages of bacteria. These two closely related sponges from different oceans provide a unique opportunity to examine the evolution of sponge-associated bacterial communities. Mitochondrial cytochrome oxidase subunit I gene sequences fromX.mutaandX.testudinariashowed little divergence between the two species. A detailed analysis of the bacterial communities associated with these sponges, comprising over 900 full-length 16S rRNA gene sequences, revealed remarkable similarity in the bacterial communities of the two species. Both sponge-associated communities include sequences found only in the twoXestospongiaspecies, as well as sequences found also in other sponge species and are dominated by three bacterial groups,Chloroflexi,Acidobacteria, andActinobacteria. While these groups consistently dominate the bacterial communities revealed by 16S rRNA gene-based analysis of sponge-associated bacteria, the depth of sequencing undertaken in this study revealed clades of bacteria specifically associated with each of the twoXestospongiaspecies, and also with the genusXestospongia, that have not been found associated with other sponge species or other ecosystems. This study, comparing the bacterial communities associated with closely related but geographically distant sponge hosts, gives new insight into the intimate relationships between marine sponges and some of their bacterial symbionts.

scholarly journals Epipelic cyanobacterial diversity in Pinang River basin, Malaysia, revealed by 16S-based metagenomic approach

Algologia ◽  
2021 ◽  
Vol 31 (1) ◽  
pp. 93-113
Author(s):  
A.R. Nur Fadzliana ◽  
◽  
W.O. Wan Maznah ◽  
S.A.M. Nor ◽  
Choon Pin Foong ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
River Basin ◽  
Sequence Data ◽  
Diversity Index ◽  
Saline Water ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Cyanobacterial Community ◽  
Upstream Station

Cyanobacteria are the most widespread group of photosynthetic prokaryotes. They are primary producers in a wide variety of habitats and are able to thrive in harsh environments, including polluted waters; therefore, this study was conducted to explore the cyanobacterial populations inhabiting river tributaries with different levels of pollution. Sediment samples (epipelon) were collected from selected tributaries of the Pinang River basin. Air Terjun (T1) and Air Itam rivers (T2) represent the upper streams of Pinang River basin, while Dondang (T3) and Jelutong rivers (T4) are located at in the middle of the river basin. The Pinang River (T5) is located near the estuary and is subjected to saline water intrusion during high tides. Cyanobacterial community was determined by identifying the taxa via 16S rRNA gene amplicon sequence data. 16S rRNA gene amplicons generated from collected samples were sequenced using illumina Miseq, with the targeted V3 and V4 regions yielding approximately 1 mln reads per sample. Synechococcus, Phormidium, Arthronema and Leptolyngbya were found in all samples. Shannon-Weiner diversity index was highest (H’ = 1.867) at the clean upstream station (T1), while the moderately polluted stream (T3) recorded the lowest diversity (H’ = 0.399), and relatively polluted stations (T4 and T5) recorded fairly high values of H’. This study provides insights into the cyanobacterial community structure in Pinang River basin via cultivation-independent techniques using 16S rRNA gene amplicon sequence. Occurrence of some morphospecies at specific locations showed that the cyanobacterial communities are quite distinct and have specific ecological demands. Some species which were ubiquitous might be able to tolerate varied environmental conditions.

scholarly journals Three novel lineages of ‘Candidatus Liberibacter africanus’ associated with native rutaceous hosts of Trioza erytreae in South Africa

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 723-731 ◽  
Author(s):  
Ronel Roberts ◽  
Emma T. Steenkamp ◽  
Gerhard Pietersen
Keyword(s):  
South Africa ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Nucleotide Sequence Data ◽  
Trioza Erytreae

Greening disease of citrus in South Africa is associated with ‘Candidatus Liberibacter africanus’ (Laf), a phloem-limited bacterium vectored by the sap-sucking insect Trioza erytreae (Triozidae). Despite the implementation of control strategies, this disease remains problematic, suggesting the existence of reservoir hosts to Laf. The current study aimed to identify such hosts. Samples from 234 trees of Clausena anisata, 289 trees of Vepris lanceolata and 231 trees of Zanthoxylum capense were collected throughout the natural distribution of these trees in South Africa. Total DNA was extracted from samples and tested for the presence of liberibacters by a generic Liberibacter TaqMan real-time PCR assay. Liberibacters present in positive samples were characterized by amplifying and sequencing rplJ, omp and 16S rRNA gene regions. The identity of tree host species from which liberibacter sequences were obtained was verified by sequencing host rbcL genes. Of the trees tested, 33 specimens of Clausena, 17 specimens of Vepris and 10 specimens of Zanthoxylum tested positive for liberibacter. None of the samples contained typical citrus-infecting Laf sequences. Phylogenetic analysis of 16S rRNA gene sequences indicated that the liberibacters obtained from Vepris and Clausena had 16S rRNA gene sequences identical to that of ‘Candidatus Liberibacter africanus subsp. capensis’ (LafC), whereas those from Zanthoxylum species grouped separately. Phylogenetic analysis of the rplJ and omp gene regions revealed unique clusters for liberibacters associated with each tree species. We propose the following names for these novel liberibacters: ‘Candidatus Liberibacter africanus subsp. clausenae’ (LafCl), ‘Candidatus Liberibacter africanus subsp. vepridis’ (LafV) and ‘Candidatus Liberibacter africanus subsp. zanthoxyli’ (LafZ). This study did not find any natural hosts of Laf associated with greening of citrus. While native citrus relatives were shown to be infected with Laf-related liberibacters, nucleotide sequence data suggest that these are not alternative sources of Laf to citrus orchards, per se.

scholarly journals Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Marc A. Sze ◽  
Begüm D. Topçuoğlu ◽  
Nicholas A. Lesniak ◽  
Mack T. Ruffin ◽  
Patrick D. Schloss
Keyword(s):  
Colorectal Cancer ◽  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Short Chain Fatty Acids ◽  
Tumor Burden ◽  
Short Chain ◽  
Rrna Gene ◽  
Chain Fatty Acids

ABSTRACT Colonic bacterial populations are thought to have a role in the development of colorectal cancer with some protecting against inflammation and others exacerbating inflammation. Short-chain fatty acids (SCFAs) have been shown to have anti-inflammatory properties and are produced in large quantities by colonic bacteria that produce SCFAs by fermenting fiber. We assessed whether there was an association between fecal SCFA concentrations and the presence of colonic adenomas or carcinomas in a cohort of individuals using 16S rRNA gene and metagenomic shotgun sequence data. We measured the fecal concentrations of acetate, propionate, and butyrate within the cohort and found that there were no significant associations between SCFA concentration and tumor status. When we incorporated these concentrations into random forest classification models trained to differentiate between people with healthy colons and those with adenomas or carcinomas, we found that they did not significantly improve the ability of 16S rRNA gene or metagenomic gene sequence-based models to classify individuals. Finally, we generated random forest regression models trained to predict the concentration of each SCFA based on 16S rRNA gene or metagenomic gene sequence data from the same samples. These models performed poorly and were able to explain at most 14% of the observed variation in the SCFA concentrations. These results support the broader epidemiological data that questions the value of fiber consumption for reducing the risks of colorectal cancer. Although other bacterial metabolites may serve as biomarkers to detect adenomas or carcinomas, fecal SCFA concentrations have limited predictive power. IMPORTANCE Considering that colorectal cancer is the third leading cancer-related cause of death within the United States, it is important to detect colorectal tumors early and to prevent the formation of tumors. Short-chain fatty acids (SCFAs) are often used as a surrogate for measuring gut health and for being anticarcinogenic because of their anti-inflammatory properties. We evaluated the fecal SCFA concentrations of a cohort of individuals with different colonic tumor burdens who were previously analyzed to identify microbiome-based biomarkers of tumors. We were unable to find an association between SCFA concentration and tumor burden or use SCFAs to improve our microbiome-based models of classifying people based on their tumor status. Furthermore, we were unable to find an association between the fecal community structure and SCFA concentrations. Our results indicate that the association between fecal SCFAs, the gut microbiome, and tumor burden is weak.

scholarly journals Prokaryotic taxonomy in the sequencing era and the role of MLSA in classification

2011 ◽  
Vol 32 (2) ◽  
pp. 66 ◽  
Author(s):  
Peter Kampfer ◽  
Stefanie P Glaeser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
16S Rrna Gene Sequencing ◽  
Initial Step ◽  
Rrna Gene ◽  
Sequence Analyses ◽  
Phenotypic Characterisation ◽  
Novel Taxa ◽  
Rrna Gene Sequencing

The initial step in prokaryote species and genera descriptions is now largely based on the 16S rRNA gene sequencing approach followed often by a very restricted additional phenotypic characterisation of the representatives of the potential novel taxa. Despite the advantages of the sequence-based approaches, there appears to be a tendency to classify new species on the basis of comparative sequence analyses of 16S rRNA gene sequences and other gene sequence data (multilocus sequence analyses, MLSA), contrary to the indications of other data. However, the biological meaning behind these sequence data is not always clear, and one should be careful with comprehensive taxonomic rearrangements until there is better insight of these data.

scholarly journals 16S rRNA Gene Amplicon Profiling of Baby and Adult Captive Elephants in Thailand

2020 ◽  
Vol 9 (24) ◽  
Author(s):  
Sangam Kandel ◽  
Supaphen Sripiboon ◽  
Piroon Jenjaroenpun ◽  
David W. Ussery ◽  
Intawat Nookaew ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Sequence Data ◽  
Rrna Gene ◽  
Data Set ◽  
Geographical Locations

ABSTRACT Here, we present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of baby and adult elephants from four different geographical locations in Thailand. The dominant phyla among baby and adult elephants were Bacteroidetes, Firmicutes, Proteobacteria, Kiritimatiellaeota, Euryarchaeota, and Tenericutes.

scholarly journals Taxonomy of Australian clinical isolates of the genus Photorhabdus and proposal of Photorhabdus asymbiotica subsp. asymbiotica subsp. nov. and P. asymbiotica subsp. australis subsp. nov.

2004 ◽  
Vol 54 (4) ◽  
pp. 1301-1310 ◽  
Author(s):  
R. J. Akhurst ◽  
N. E. Boemare ◽  
P. H. Janssen ◽  
M. M. Peel ◽  
D. A. Alfredson ◽  
...  
Keyword(s):  
16S Rrna ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Clinical Isolates ◽  
Rrna Gene ◽  
Clinical Specimens ◽  
The Usa ◽  
Gene Sequence Data

The relationship of Photorhabdus isolates that were cultured from human clinical specimens in Australia to Photorhabdus asymbiotica isolates from human clinical specimens in the USA and to species of the genus Photorhabdus that are associated symbiotically with entomopathogenic nematodes was evaluated. A polyphasic approach that involved DNA–DNA hybridization, phylogenetic analyses of 16S rRNA and gyrB gene sequences and phenotypic characterization was adopted. These investigations showed that gyrB gene sequence data correlated well with DNA–DNA hybridization and phenotypic data, but that 16S rRNA gene sequence data were not suitable for defining species within the genus Photorhabdus. Australian clinical isolates proved to be related most closely to clinical isolates from the USA, but the two groups were distinct. A novel subspecies, Photorhabdus asymbiotica subsp. australis subsp. nov. (type strain, 9802892T=CIP 108025T=ACM 5210T), is proposed, with the concomitant creation of Photorhabdus asymbiotica subsp. asymbiotica subsp. nov. Analysis of gyrB sequences, coupled with previously published data on DNA–DNA hybridization and PCR-RFLP analysis of the 16S rRNA gene, indicated that there are more than the three subspecies of Photorhabdus luminescens that have been described and confirmed the validity of the previously proposed subdivision of Photorhabdus temperata. Although a non-luminescent, symbiotic isolate clustered consistently with P. asymbiotica in gyrB phylogenetic analyses, DNA–DNA hybridization indicated that this isolate does not belong to the species P. asymbiotica and that there is a clear distinction between symbiotic and clinical species of Photorhabdus.

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