scholarly journals Microbial Diversity of the Red Sea Urchin Loxechinus albus during Controlled Farming in Puerto Montt, Chile, Using 16S rRNA Gene Amplicon Sequencing

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Daniel A. Medina ◽  
Rudy Suárez ◽  
Marcos Godoy
Keyword(s):  
16S Rrna ◽  
Sea Urchin ◽  
Cold Water ◽  
Sea Urchins ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Rrna Sequencing ◽  
Red Sea Urchin ◽  
Loxechinus Albus

Loxechinus albus is a shallow-water sea urchin, and its distribution is related to the cold water of the Southern Hemisphere. Recently, bacterial communities, also called microbiota, in sea urchins have started being explored. In this report, we have characterized the surface, testa, and gonad microbiota using 16S rRNA sequencing.

scholarly journals Growth and Population Dynamics of the Anaerobic Fe(II)-Oxidizing and Nitrate-Reducing Enrichment Culture KS

2018 ◽  
Vol 84 (9) ◽  
Author(s):  
Claudia Tominski ◽  
Helene Heyer ◽  
Tina Lösekann-Behrens ◽  
Sebastian Behrens ◽  
Andreas Kappler
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Composition ◽  
Enrichment Culture ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Content Type ◽  
Heterotrophic Denitrification

ABSTRACTMost isolated nitrate-reducing Fe(II)-oxidizing microorganisms are mixotrophic, meaning that Fe(II) is chemically oxidized by nitrite that forms during heterotrophic denitrification, and it is debated to which extent Fe(II) is enzymatically oxidized. One exception is the chemolithoautotrophic enrichment culture KS, a consortium consisting of a dominant Fe(II) oxidizer,Gallionellaceaesp., and less abundant heterotrophic strains (e.g.,Bradyrhizobiumsp.,Nocardioidessp.). Currently, this is the only nitrate-reducing Fe(II)-oxidizing culture for which autotrophic growth has been demonstrated convincingly for many transfers over more than 2 decades. We used 16S rRNA gene amplicon sequencing and physiological growth experiments to analyze the community composition and dynamics of culture KS with various electron donors and acceptors. Under autotrophic conditions, an operational taxonomic unit (OTU) related to known microaerophilic Fe(II) oxidizers within the familyGallionellaceaedominated culture KS. With acetate as an electron donor, most 16S rRNA gene sequences were affiliated withBradyrhizobiumsp.Gallionellaceaesp. not only was able to oxidize Fe(II) under autotrophic and mixotrophic conditions but also survived over several transfers of the culture on only acetate, although it then lost the ability to oxidize Fe(II).Bradyrhizobiumspp. became and remained dominant when culture KS was cultivated for only one transfer under heterotrophic conditions, even when conditions were reverted back to autotrophic in the next transfer. This study showed a dynamic microbial community in culture KS that responded to changing substrate conditions, opening up questions regarding carbon cross-feeding, metabolic flexibility of the individual strains in KS, and the mechanism of Fe(II) oxidation by a microaerophile in the absence of O2.IMPORTANCENitrate-reducing Fe(II)-oxidizing microorganisms are present in aquifers, soils, and marine and freshwater sediments. Most nitrate-reducing Fe(II) oxidizers known are mixotrophic, meaning that they need organic carbon to continuously oxidize Fe(II) and grow. In these microbes, Fe(II) was suggested to be chemically oxidized by nitrite that forms during heterotrophic denitrification, and it remains unclear whether or to what extent Fe(II) is enzymatically oxidized. In contrast, the enrichment culture KS was shown to oxidize Fe(II) autotrophically coupled to nitrate reduction. This culture contains the designated Fe(II) oxidizerGallionellaceaesp. and several heterotrophic strains (e.g.,Bradyrhizobiumsp.). We showed that culture KS is able to metabolize Fe(II) and a variety of organic substrates and is able to adapt to dynamic environmental conditions. When the community composition changed andBradyrhizobiumbecame the dominant community member, Fe(II) was still oxidized byGallionellaceaesp., even when culture KS was cultivated with acetate/nitrate [Fe(II) free] before being switched back to Fe(II)/nitrate.

scholarly journals 16S rRNA Gene Amplicon Sequencing Data of Tailing and Nontailing Rhizosphere Soils of Mimosa pudica from a Heavy Metal-Contaminated Ex-Tin Mining Area

2020 ◽  
Vol 9 (42) ◽  
Author(s):  
Saidu Abdullahi ◽  
Hazzeman Haris ◽  
Kamarul Z. Zarkasi ◽  
Hamzah G. Amir
Keyword(s):  
Heavy Metal ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Mimosa Pudica ◽  
Sequencing Data ◽  
Content Type ◽  
Rhizosphere Soils

ABSTRACT The 16S rRNA gene amplicon sequence data from tailing and nontailing rhizosphere soils of Mimosa pudica from a heavy metal-contaminated area are reported here. Diverse bacterial taxa were represented in the results, and the most dominant phyla were Proteobacteria (41.2%), Acidobacteria (17.1%), and Actinobacteria (14.4%).

scholarly journals Arenicella chitinivorans sp. nov., a gammaproteobacterium isolated from the sea urchin Strongylocentrotus intermedius

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4124-4129 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Ilse Cleenwerck ◽  
Natalia V. Zhukova ◽  
Seung Bum Kim ◽  
Paul de Vos
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Urchin ◽  
Type Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A strictly aerobic, Gram-stain-negative, rod-shaped, non-motile and yellow-pigmented bacterial strain, designated KMM 6208T, was isolated from a sea urchin. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that this novel isolate was affiliated to the class Gammaproteobacteria and formed a robust cluster with Arenicella xantha KMM 3895T with 98.2 % 16S rRNA gene sequence similarity. Strain KMM 6208T grew in the presence of 0.5–5 % NaCl and at a temperature range of 4–38 °C. The isolate was oxidase-positive and hydrolysed aesculin, casein, chitin, gelatin, starch and Tweens 40 and 80. The prevalent fatty acids of strain KMM 6208T were C16 : 1ω7c, iso-C16 : 0, iso-C18 : 0, C18 : 1ω7c and C16 : 0. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified aminophospholipid, and the major isoprenoid quinone was Q-8. The DNA G+C content of strain KMM 6208T was 46.3 mol%. The DNA–DNA relatedness value of strain KMM 6208T with Arenicella xantha KMM 3895T was 5 %. Molecular data in a combination with phenotypic findings strongly suggest inclusion of this novel strain in the genus Arenicella as a representative of a novel species for which the name Arenicella chitinivorans sp. nov. is proposed. The type strain is KMM 6208T ( = KCTC 12711T = LMG 26983T).

scholarly journals 16S rRNA Gene Amplicon Sequencing of Gut Microbiota from Naked Carp (Gymnocypris przewalskii) in Qinghai Lake, China

2021 ◽  
Vol 10 (23) ◽  
Author(s):  
Fayan Wang ◽  
Yu Liu ◽  
Guangxin Li ◽  
Xi Yang ◽  
Qiang Gao
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
Qinghai Lake ◽  
Second Grade ◽  
Rrna Gene ◽  
Content Type ◽  
Gymnocypris Przewalskii ◽  
State Protection

Naked carp ( Gymnocypris przewalskii ) is a second-grade animal under state protection of China. We report 16S rRNA gene amplicon analysis of the gut microbiota of Gymnocypris przewalskii . The three most abundant phyla are Tenericutes , Proteobacteria , and Fusobacteria , and the six most abundant genera are Aeromonas , Clostridium , Cetobacterium , Shewanella , Prochlorococcus , and Vibrio .

scholarly journals Frigidibacter albus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from lake water

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1199-1206 ◽  
Author(s):  
Ai-Hua Li ◽  
Yu-Guang Zhou
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Cold Water ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

Three Gram-staining-negative, strictly aerobic, non-pigmented, non-motile, rod-shaped bacterial strains, SP32T ( = SLM-1T), SR68 ( = SLM-3) and SP95 ( = SLM-2), were isolated from two water samples of a cold-water lake in Xinjiang province, China. Growth was observed at 4–25 °C and pH 6.0–9.0, and optimum growth occurred at 18–20 °C and at pH 7.0–7.5. Phylogenetic analysis of 16S rRNA gene sequences revealed that these isolates belonged to the family Rhodobacteraceae , but formed an evolutionary lineage distinct from other species of this family with validly published names. Strain SP32T showed the highest 16S rRNA gene sequence similarity (96.7 %) to Rhodobacter veldkampii ATCC 35703T, and the similarity to members of the genera Defluviimonas , Haematobacter and Pseudorhodobacter was respectively 95.8–96.4, 96.0–96.1 and 95.3–96.1 %. The genomic DNA G+C content of strain SP32T was 67.6 mol%. The major fatty acids (>5 %) were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) and11-methyl C18 : 1ω7c. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and one unidentified polar lipid were the main polar lipids. Ubiquinone 10 (Q-10) was the sole respiratory quinone. Strain SP32T did not produce photosynthetic pigments and did not contain the gene pufM, by which it differed from the phototrophic species of the family Rhodobacteraceae . Based on its distinct phenotypic, chemotaxonomic and phylogenetic properties, strain SP32T represents a novel species in a novel genus within the family Rhodobacteraceae , for which we propose the name Frigidibacter albus gen. nov., sp. nov. The type strain of Frigidibacter albus is strain SP32T ( = SLM-1T = CGMCC 1.13995T = NBRC 109671T).

scholarly journals Bacterial Diversity Profiling of the New Zealand Parasitic Blowfly Lucilia sericata Based on 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (19) ◽  
Author(s):  
Nikola Palevich ◽  
Paul H. Maclean ◽  
Luis Carvalho ◽  
Ruy Jauregui
Keyword(s):  
New Zealand ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Sequence Data ◽  
Amplicon Sequencing ◽  
Lucilia Sericata ◽  
Rrna Gene ◽  
Data Set ◽  
Content Type

ABSTRACT Here, we present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of larval and adult Lucilia sericata, collected from Ashhurst, New Zealand (May 2020). The two dominant genera among adult male and female L. sericata were Serratia and Morganella (phylum Proteobacteria), while the larvae were also dominated by the genera Lactobacillus, Carnobacterium, and Lactococcus (phylum Firmicutes).

scholarly journals Deciphering the Root Endosphere Microbiome of the Desert Plant Alhagi sparsifolia for Drought Resistance-Promoting Bacteria

2020 ◽  
Vol 86 (11) ◽  
Author(s):  
Lei Zhang ◽  
Weipeng Zhang ◽  
Qiqi Li ◽  
Rui Cui ◽  
Zhuo Wang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Drought Resistance ◽  
Amplicon Sequencing ◽  
Disease Suppression ◽  
Rrna Gene ◽  
Desert Plant ◽  
Desert Plants ◽  
Alhagi Sparsifolia ◽  
Content Type

ABSTRACT Drought is among the most destructive abiotic stresses limiting crop growth and yield worldwide. Although most research has focused on the contribution of plant-associated microbial communities to plant growth and disease suppression, far less is known about the microbes involved in drought resistance among desert plants. In the present study, we applied 16S rRNA gene amplicon sequencing to determine the structure of rhizosphere and root endosphere microbiomes of Alhagi sparsifolia. Compared to those of the rhizosphere, endosphere microbiomes had lower diversity but contained several taxa with higher relative abundance; many of these taxa were also present in the roots of other desert plants. We isolated a Pseudomonas strain (LTGT-11-2Z) that was prevalent in root endosphere microbiomes of A. sparsifolia and promoted drought resistance during incubation with wheat. Complete genome sequencing of LTGT-11-2Z revealed 1-aminocyclopropane-1-carboxylate deaminases, siderophore, spermidine, and colanic acid biosynthetic genes, as well as type VI secretion system (T6SS) genes, which are likely involved in biofilm formation and plant-microbe interactions. Together, these results indicate that drought-enduring plants harbor bacterial endophytes favorable to plant drought resistance, and they suggest that novel endophytic bacterial taxa and gene resources may be discovered among these desert plants. IMPORTANCE Understanding microbe-mediated plant resistance to drought is important for sustainable agriculture. We performed 16S rRNA gene amplicon sequencing and culture-dependent functional analyses of Alhagi sparsifolia rhizosphere and root endosphere microbiomes and identified key endophytic bacterial taxa and their genes facilitating drought resistance in wheat. This study improves our understanding of plant drought resistance and provides new avenues for drought resistance improvement in crop plants under field conditions.

scholarly journals Myceligenerans cantabricum sp. nov., a barotolerant actinobacterium isolated from a deep cold-water coral

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1328-1334 ◽  
Author(s):  
Aida Sarmiento-Vizcaíno ◽  
Verónica González ◽  
Alfredo F. Braña ◽  
Axayacatl Molina ◽  
José L. Acuña ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Cold Water ◽  
Micrococcus Luteus ◽  
Antibiotic Production ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

An actinobacterium strain (M-201T) was isolated from a deep-sea scleractinian coral (Fam. Caryophillidae) collected at 1500 m depth in the Avilés Canyon in the Cantabrian Sea, Asturias, Spain. Strain M-201T grew at pH 6.0–9.0 (optimum pH 7.0), between 4 and 37 °C (optimum 28 °C) and at salinities of 0.5–10.5 % (w/v) NaCl (optimum 0.5–3.0 %). The peptidoglycan contained the amino acids Lys, Ala, Thr, Glu and one unknown amino acid component, and belonged to type A4α, and the cell-wall sugars are glucose, mannose and galactose. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unknown phosphoglycolipid and seven unknown glycolipids. The predominant menaquinones were MK-9(H4) and MK-9(H6). Major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 72.4 mol%. The chemotaxonomic properties supported the affiliation of strain M-201T to the genus Myceligenerans . Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism was most closely related to Myceligenerans crystallogenes CD12E2-27T (98.2 % 16S rRNA gene sequence similarity). However, it had a relatively low DNA–DNA relatedness value with the above strain (48 %). The isolate showed antibiotic activity against Escherichia coli , Micrococcus luteus ATCC 14452 and Saccharomyces cerevisiae var. carlsbergensis. To the best of our knowledge, this is the first report of antibiotic production in the genus Myceligenerans . The differences in phenotypic, metabolic, ecological and phylogenetic characteristics justify the proposal of a novel species of the genus Myceligenerans , Myceligenerans cantabricum sp. nov., with M-201T ( = CECT 8512T = DSM 28392T) as the type strain.

scholarly journals Microbiomes of Field-Grown Maize and Soybean in Southeastern and Central Brazil Inferred by High-Throughput 16S and Internal Transcribed Spacer Amplicon Sequencing

2021 ◽  
Vol 10 (31) ◽  
Author(s):  
Maike Rossmann ◽  
Andrew Maltez Thomas ◽  
Suzana Sato Guima ◽  
Layla Farage Martins ◽  
Patrik Inderbitzin ◽  
...  
Keyword(s):  
16S Rrna ◽  
Internal Transcribed Spacer ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Its Sequencing ◽  
Field Soil ◽  
Sequencing Data ◽  
Content Type ◽  
Central Brazil ◽  
Soybean Plants

We report the microbial 16S rRNA gene and internal transcribed spacer (ITS) sequencing data of maize and soybean plants and field soil from eight locations in Brazil. Enterobacter and Pseudomonas were among the most abundant genera. The data suggest the presence of several species that have not been documented for Brazil.

scholarly journals De novo Assembly and Analysis of Tissue-Specific Transcriptomes of the Edible Red Sea Urchin Loxechinus albus Using RNA-Seq

Biology ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 995
Author(s):  
Paulette Antiqueo ◽  
Rodrigo Zuloaga ◽  
Macarena Bastias-Molina ◽  
Claudio Meneses ◽  
Juan Manuel Estrada ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Red Sea ◽  
De Novo ◽  
Sea Urchins ◽  
Expression Profiles ◽  
Natural Populations ◽  
Gc Content ◽  
Illumina Platform ◽  
Red Sea Urchin ◽  
Loxechinus Albus

Edible red sea urchin (Loxechinus albus) is an endemic echinoderm species of the Chilean coasts. The worldwide demand for high-quality gonads of this species has addressed the depletion of its natural populations. Studies on this sea urchin are limited, and genomic information is almost nonexistent. Hence, generate a transcriptome is crucial information that will considerably enrich molecular data and promote future findings for the L. albus aquaculture. Here, we obtained transcriptomic data of the edible red sea urchin by Illumina platform. Total RNA was extracted from gonads, intestines, and coelomocytes of juvenile urchins, and samples were sequenced using MiSeq Illumina technology. A total of 91,119,300 paired-end reads were de novo assembled, 185,239 transcripts produced, and a reference transcriptome created with 38.8% GC content and an N50 of 1769 bp. Gene ontology analysis revealed notable differences in the expression profiles between gonads, intestines, and coelomocytes, allowing the detection of transcripts associated with specific biological processes and KEGG pathways. These data were validated using 12 candidate transcripts by real-time qPCR. This dataset will provide a valuable molecular resource for L. albus and other species of sea urchins.

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