scholarly journals The Purple Sea Urchin Strongylocentrotus purpuratus Demonstrates a Compartmentalization of Gut Bacterial Microbiota, Predictive Functional Attributes, and Taxonomic Co-Occurrence

2019 ◽  
Vol 7 (2) ◽  
pp. 35 ◽  
Author(s):  
Joseph Hakim ◽  
Julie Schram ◽  
Aaron Galloway ◽  
Casey Morrow ◽  
Michael Crowley ◽  
...  
Keyword(s):  
Sea Urchin ◽  
High Throughput Sequencing ◽  
Sea Urchins ◽  
Community Integration ◽  
Strongylocentrotus Purpuratus ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Tide Pool ◽  
Alpha And Beta Diversity ◽  
Taxonomic Organization

The sea urchin Strongylocentrotus purpuratus (order Camarodonta, family Strongylocentrotidae) can be found dominating low intertidal pool biomass on the southern coast of Oregon, USA. In this case study, three adult sea urchins were collected from their shared intertidal pool, and the bacteriome of their pharynx, gut tissue, and gut digesta, including their tide pool water and algae, was determined using targeted high-throughput sequencing (HTS) of the 16S rRNA genes and bioinformatics tools. Overall, the gut tissue demonstrated Arcobacter and Sulfurimonas (Epsilonproteobacteria) to be abundant, whereas the gut digesta was dominated by Psychromonas (Gammaproteobacteria), Propionigenium (Fusobacteria), and Flavobacteriales (Bacteroidetes). Alpha and beta diversity analyses indicated low species richness and distinct microbial communities comprising the gut tissue and digesta, while the pharynx tissue had higher richness, more closely resembling the water microbiota. Predicted functional profiles showed Kyoto Encyclopedia of Genes and Genomes (KEGG) Level-2 categories of energy metabolism, membrane transport, cell motility, and signal transduction in the gut tissue, and the gut digesta represented amino acid, carbohydrate, vitamin and cofactor metabolisms, and replication and repair. Co-occurrence network analysis showed the potential relationships and key taxa, such as the highly abundant Arcobacter and Propionigenium, influencing population patterns and taxonomic organization between the gut tissue and digesta. These results demonstrate a trend of microbial community integration, allocation, predicted metabolic roles, and taxonomic co-occurrence patterns in the S. purpuratus gut ecosystem.

scholarly journals Effects of five southern California macroalgal diets on consumption, growth, and gonad weight, in the purple sea urchin Strongylocentrotus purpuratus

2014 ◽  
Author(s):  
Matthew C Foster ◽  
Jarrett E Byrnes ◽  
Daniel C Reed
Keyword(s):  
Sea Urchin ◽  
Sea Urchins ◽  
Strongylocentrotus Purpuratus ◽  
Macrocystis Pyrifera ◽  
Reproductive Capacity ◽  
Giant Kelp ◽  
Mixed Diet ◽  
Gonad Weight ◽  
Consumption Growth ◽  
Purple Sea Urchin

Consumer growth and reproductive capacity are direct functions of diet. Strongylocentrotid sea urchins, the dominant herbivores in California kelp forests, strongly prefer giant kelp (Macrocystis pyrifera), but are highly catholic in their ability to consume other species. The biomass of Macrocystis fluctuates greatly in space and time and the extent to which urchins can use alternate species of algae or a mixed diet of multiple algal species to maintain fitness when giant kelp is unavailable is unknown. We experimentally examined the effects of single and mixed species diets on consumption, growth and gonad weight in the purple sea urchin Strongylocentrotus purpuratus. Urchins were fed single species diets consisting of one of four common species of macroalgae (the kelps Macrocystis pyrifera and Pterygophora californica, and the red algae Chondracanthus corymbiferus and Rhodymenia californica (hereafter referred to by genus) or a mixed diet containing all four species ad libitum over a 13-week period in a controlled laboratory setting. Urchins fed Chondracanthus, Macrocystis and a mixed diet showed the highest growth (in terms of test diameter, wet weight and jaw length) and gonad weight while urchins fed Pterygophora and Rhodymenia showed the lowest. Urchins consumed their preferred food, Macrocystis at the highest rate when offered a mixture, but consumed Chondracanthus or Macrocystis at similar rates when the two algae were offered alone. The differences in urchin feeding behavior and growth observed between these diet types suggest the relative availability of the algae tested here could affect urchin populations and their interactions with the algal assemblage. The fact that the performance of urchins fed Chondracanthus was similar or higher than those fed the preferred Macrocystis suggests purple sea urchins could sustain growth and reproduction during times of low Macrocystis abundance as is common following large wave events.

scholarly journals Comparative Analysis of the Fecal Bacterial Microbiota of Wintering Whooper Swans (Cygnus Cygnus)

2021 ◽  
Vol 8 ◽  
Author(s):  
Wenxia Wang ◽  
Songlin Huang ◽  
Liangliang Yang ◽  
Guogang Zhang
Keyword(s):  
Intestinal Microbiota ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
The Body ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Illumina Hiseq ◽  
Linear Discriminant ◽  
Bacterial Microbiota ◽  
And Control

There are many and diverse intestinal microbiota, and they are closely related to various physiological functions of the body. They directly participate in the host's food digestion, nutrient absorption, energy metabolism, immune response, and many other physiological activities and are also related to the occurrence of many diseases. The intestinal microbiota are extremely important for maintaining normal physical health. In order to explore the composition and differences of the intestinal microbiota of whooper swans in different wintering areas, we collected fecal samples of whooper swans in Sanmenxia, Henan, and Rongcheng, Shandong, and we used the Illumina HiSeq platform to perform high-throughput sequencing of bacterial 16S rRNA genes. Comparison between Sanmenxia and Rongcheng showed no significant differences in ACE, Chao 1, Simpson, and Shannon indices (p > 0.05). Beta diversity results showed significant differences in bacterial communities between two groups [analysis of similarity (ANOSIM): R = 0.80, p = 0.011]. Linear discriminant analysis effect size (LEfSe) analysis showed that at the phylum level, the relative abundance of Actinobacteria was significantly higher in Sanmenxia whooper swans than Rongcheng whooper swans. At the genus level, the amount of Psychrobacter and Carnobacterium in Sanmenxia was significantly higher in Rongcheng, while the relative abundance Catellicoccus and Lactobacillus was significantly higher in Rongcheng than in Sanmenxia. This study analyzed the composition, characteristics, and differences of the intestinal microbiota of the whooper swans in different wintering environments and provided theoretical support for further exploring the relationship between the intestinal microbiota of the whooper swans and the external environment. And it played an important role in the overwintering physiology and ecology, population management, and epidemic prevention and control of whooper swans.

scholarly journals Vitellibacter echinoideorum sp. nov., isolated from a sea urchin (Tripneustes gratilla)

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2320-2325 ◽  
Author(s):  
Shih-Yao Lin ◽  
Asif Hameed ◽  
Cheng-Zhe Wen ◽  
You-Cheng Liu ◽  
Yi-Han Hsu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sea Urchins ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The Novel ◽  
Moderate Amount ◽  
Polar Lipid Profile

A Gram-stain-negative, aerobic, rod-shaped, yellow-pigment-producing bacterium (designated strain CC-CZW007T) was isolated from seafood samples (sea urchins) at Penghu Island in Taiwan. Strain CC-CZW007T grew optimally at pH 7.0 and 30 °C in the presence of 3 % (w/v) NaCl. The novel strain shared highest 16S rRNA gene sequence similarity to Vitellibacter vladivostokensis JCM 11732T (96.8 %), Vitellibacter soesokkakensis KCTC 32536T (96.4 %), Vitellibacter nionensis KCTC 32420T (95.8 %) and Vitellibacter aestuarii JCM 15496T (95.6 %) and lower sequence similarity to members of other genera. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CZW007T with respect to other species of the genus Vitellibacter. The major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipid profile was composed of major amounts of phosphatidylethanolamine, unidentified lipids and aminolipids; a moderate amount of aminophospholipid was also detected. The DNA G+C content was 34.7 mol%. The predominant quinone system was menaquinone (MK-6). On the basis of polyphasic taxonomic evidence presented here, strain CC-CZW007T is proposed to represent a novel species within the genus Vitellibacter, for which the name Vitellibacter echinoideorum sp. nov. is proposed. The type strain is CC-CZW007T ( = BCRC 80886T = JCM 30378T).

scholarly journals Illumina-based sequencing analysis of pathogenic microorganisms in dental caries patients of different Chinese ethnic groups

2019 ◽  
Vol 47 (10) ◽  
pp. 5037-5047
Author(s):  
Chen Yun ◽  
Li Zhiyan ◽  
Zhao Chong ◽  
Liu Jing ◽  
Zhang Xin ◽  
...  
Keyword(s):  
Dental Caries ◽  
Ethnic Groups ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Control Group ◽  
Sequencing Analysis ◽  
Pathogenic Microorganisms ◽  
Effective Prevention

Objective To analyze the pathogenic community diversity of dental caries patients from Tu, Hui, Tibetan, and Han Chinese ethnic groups. Methods Forty saliva samples were collected from the following patients with dental caries: Tu from Huzhu County (n = 10), Hui from Ping’an County (n = 10), Han from Xining city (n = 10), and Tibetan from Yushu (n = 10). High-throughput sequencing of bacterial 16S rRNA genes (V3-V4) was performed using the Illumina MiSeq sequencing platform. Results Based on 97% similarity clustering, operational taxonomic units of Tu, Hui, Tibetan, and Han ethnic groups were 181, 210, 38, and 67, respectively. In Tu patients, 11 phyla, 19 classes, and 89 genera were identified, compared with 13 phyla, 21 classes, and 113 genera in Hui patients, two phyla, four classes, and 21 genera in Tibetan patients, five phyla, nine classes, and 34 genera in Han patients, and four phyla, five classes, and 12 genera from the control group. The main pathogens of dental caries included Veillonella, Aggregatibacter, Leptotrichia, Bacteroides, Granulicatella, Streptococcus, and Prevotella. Conclusion The pathogenic microorganisms of dental caries differ greatly among Tu, Hui, Tibetan, and Han ethnic groups. These findings provide a theoretical basis for the effective prevention and treatment of dental caries in different Chinese populations.

scholarly journals Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane

Archaea ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-14
Author(s):  
Wei-Yu Chen ◽  
Lucia Kraková ◽  
Jer-Horng Wu ◽  
Domenico Pangallo ◽  
Lenka Jeszeová ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
High Throughput Sequencing ◽  
Molecular Techniques ◽  
Upflow Anaerobic Sludge Blanket ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Uasb Reactor ◽  
Anaerobic Sludge ◽  
Methane Formation ◽  
Proteomic Approach

Tetramethylammonium-degrading methanogenic consortia from a complete-mixing suspended sludge (CMSS) and an upflow anaerobic sludge blanket (UASB) reactors were studied using multiple PCR-based molecular techniques and shotgun proteomic approach. The prokaryotic 16S rRNA genes of the consortia were analyzed by quantitative PCR, high-throughput sequencing, and DGGE-cloning methods. The results showed that methanogenicarchaeawere highly predominant in both reactors but differed markedly according to community structure. Community and proteomic analysis revealed thatMethanomethylovoransandMethanosarcinawere the major players for the demethylation of methylated substrates and methane formation through the reduction pathway of methyl-S-CoM and possibly, acetyl-CoA synthase/decarbonylase-related pathways. Unlike high dominance of oneMethanomethylovoranspopulation in the CMSS reactor, diverse methylotrophicMethanosarcinaspecies inhabited in syntrophy-like association with hydrogenotrophicMethanobacteriumin the granular sludge of UASB reactor. The overall findings indicated the reactor-dependent community structures of quaternary amines degradation and provided microbial insight for the improved understanding of engineering application.

scholarly journals Status of the Archaeal and Bacterial Census: an Update

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Patrick D. Schloss ◽  
Rene A. Girard ◽  
Thomas Martin ◽  
Joshua Edwards ◽  
J. Cameron Thrash
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity ◽  
High Throughput Sequencing ◽  
New Technologies ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Short Read ◽  
Sequencing Technologies

ABSTRACT A census is typically carried out for people across a range of geographical levels; however, microbial ecologists have implemented a molecular census of bacteria and archaea by sequencing their 16S rRNA genes. We assessed how well the census of full-length 16S rRNA gene sequences is proceeding in the context of recent advances in high-throughput sequencing technologies because full-length sequences are typically used as references for classification of the short sequences generated by newer technologies. Among the 1,411,234 and 53,546 full-length bacterial and archaeal sequences, 94.5% and 95.1% of the bacterial and archaeal sequences, respectively, belonged to operational taxonomic units (OTUs) that have been observed more than once. Although these metrics suggest that the census is approaching completion, 29.2% of the bacterial and 38.5% of the archaeal OTUs have been observed more than once. Thus, there is still considerable diversity to be explored. Unfortunately, the rate of new full-length sequences has been declining, and new sequences are primarily being deposited by a small number of studies. Furthermore, sequences from soil and aquatic environments, which are known to be rich in bacterial diversity, represent only 7.8 and 16.5% of the census, while sequences associated with host-associated environments represent 55.0% of the census. Continued use of traditional approaches and new technologies such as single-cell genomics and short-read assembly are likely to improve our ability to sample rare OTUs if it is possible to overcome this sampling bias. The success of ongoing efforts to use short-read sequencing to characterize archaeal and bacterial communities requires that researchers strive to expand the depth and breadth of this census. IMPORTANCE The biodiversity contained within the bacterial and archaeal domains dwarfs that of the eukaryotes, and the services these organisms provide to the biosphere are critical. Surprisingly, we have done a relatively poor job of formally tracking the quality of the biodiversity as represented in full-length 16S rRNA genes. By understanding how this census is proceeding, it is possible to suggest the best allocation of resources for advancing the census. We found that the ongoing effort has done an excellent job of sampling the most abundant organisms but struggles to sample the rarer organisms. Through the use of new sequencing technologies, we should be able to obtain full-length sequences from these rare organisms. Furthermore, we suggest that by allocating more resources to sampling environments known to have the greatest biodiversity, we will be able to make significant advances in our characterization of archaeal and bacterial diversity.

scholarly journals Distribution of Hydrogen-Producing Bacteria in Tibetan Hot Springs, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Li Ma ◽  
Geng Wu ◽  
Jian Yang ◽  
Liuqin Huang ◽  
Dorji Phurbu ◽  
...  
Keyword(s):  
Community Structure ◽  
Hydrogen Production ◽  
16S Rrna ◽  
High Throughput Sequencing ◽  
Hot Springs ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The Tibetan Plateau

Investigating the distribution of hydrogen-producing bacteria (HPB) is of great significance to understanding the source of biological hydrogen production in geothermal environments. Here, we explored the compositions of HPB populations in the sediments of hot springs from the Daggyai, Quzhuomu, Quseyongba, and Moluojiang geothermal zones on the Tibetan Plateau, with the use of Illumina MiSeq high-throughput sequencing of 16S rRNA genes and hydA genes. In the present study, the hydA genes were successfully amplified from the hot springs with a temperature of 46–87°C. The hydA gene phylogenetic analysis showed that the top three phyla of the HPB populations were Bacteroidetes (14.48%), Spirochaetes (14.12%), and Thermotogae (10.45%), while Proteobacteria were absent in the top 10 of the HPB populations, although Proteobacteria were dominant in the 16S rRNA gene sequences. Canonical correspondence analysis results indicate that the HPB community structure in the studied Tibetan hot springs was correlated with various environmental factors, such as temperature, pH, and elevation. The HPB community structure also showed a spatial distribution pattern; samples from the same area showed similar community structures. Furthermore, one HPB isolate affiliated with Firmicutes was obtained and demonstrated the capacity of hydrogen production. These results are important for us to understand the distribution and function of HPB in hot springs.

scholarly journals Novel Universal Primers for Metabarcoding eDNA Surveys of Marine Mammals and Other Marine Vertebrates

2019 ◽  
Author(s):  
Elena Valsecchi ◽  
Jonas Bylemans ◽  
Simon J. Goodman ◽  
Roberto Lombardi ◽  
Ian Carr ◽  
...  
Keyword(s):  
Marine Mammals ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Taxonomic Resolution ◽  
Universal Primers ◽  
Marine Biodiversity ◽  
Primer Sets ◽  
Marine Megafauna

ABSTRACTMetabarcoding studies using environmental DNA (eDNA) and high throughput sequencing (HTS) are rapidly becoming an important tool for assessing and monitoring marine biodiversity, detecting invasive species, and supporting basic ecological research. Several barcode loci targeting teleost fish and elasmobranchs have previously been developed, but to date primer sets focusing on other marine megafauna, such as marine mammals have received less attention. Similarly, there have been few attempts to identify potentially ‘universal’ barcode loci which may be informative across multiple marine vertebrate Orders. Here we describe the design and validation of four new sets of primers targeting hypervariable regions of the vertebrate mitochondrial 12S and 16S rRNA genes, which have conserved priming sites across virtually all cetaceans, pinnipeds, elasmobranchs, boney fish, sea turtles and birds, and amplify fragments with consistently high levels of taxonomically diagnostic sequence variation. ‘In silico’ validation using the OBITOOLS software showed our new barcode loci outperformed most existing vertebrate barcode loci for taxon detection and resolution. We also evaluated sequence diversity and taxonomic resolution of the new barcode loci in 680 complete marine mammal mitochondrial genomes demonstrating that they are effective at resolving amplicons for most taxa to the species level. Finally, we evaluated the performance of the primer sets with eDNA samples from aquarium communities with known species composition. These new primers will potentially allow surveys of complete marine vertebrate communities in single HTS metabarcoding assessments, simplifying workflows, reducing costs, and increasing accessibility to a wider range of investigators.

scholarly journals Effects of five southern California macroalgal diets on consumption, growth, and gonad weight, in the purple sea urchin Strongylocentrotus purpuratus

2014 ◽  
Author(s):  
Matthew C Foster ◽  
Jarrett E Byrnes ◽  
Daniel C Reed
Keyword(s):  
Sea Urchin ◽  
Sea Urchins ◽  
Strongylocentrotus Purpuratus ◽  
Macrocystis Pyrifera ◽  
Reproductive Capacity ◽  
Giant Kelp ◽  
Mixed Diet ◽  
Gonad Weight ◽  
Consumption Growth ◽  
Purple Sea Urchin

Consumer growth and reproductive capacity are direct functions of diet. Strongylocentrotid sea urchins, the dominant herbivores in California kelp forests, strongly prefer giant kelp (Macrocystis pyrifera), but are highly catholic in their ability to consume other species. The biomass of Macrocystis fluctuates greatly in space and time and the extent to which urchins can use alternate species of algae or a mixed diet of multiple algal species to maintain fitness when giant kelp is unavailable is unknown. We experimentally examined the effects of single and mixed species diets on consumption, growth and gonad weight in the purple sea urchin Strongylocentrotus purpuratus. Urchins were fed single species diets consisting of one of four common species of macroalgae (the kelps Macrocystis pyrifera and Pterygophora californica, and the red algae Chondracanthus corymbiferus and Rhodymenia californica (hereafter referred to by genus) or a mixed diet containing all four species ad libitum over a 13-week period in a controlled laboratory setting. Urchins fed Chondracanthus, Macrocystis and a mixed diet showed the highest growth (in terms of test diameter, wet weight and jaw length) and gonad weight while urchins fed Pterygophora and Rhodymenia showed the lowest. Urchins consumed their preferred food, Macrocystis at the highest rate when offered a mixture, but consumed Chondracanthus or Macrocystis at similar rates when the two algae were offered alone. The differences in urchin feeding behavior and growth observed between these diet types suggest the relative availability of the algae tested here could affect urchin populations and their interactions with the algal assemblage. The fact that the performance of urchins fed Chondracanthus was similar or higher than those fed the preferred Macrocystis suggests purple sea urchins could sustain growth and reproduction during times of low Macrocystis abundance as is common following large wave events.

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