scholarly journals Characteristic Microbiomes Correlate with Polyphosphate Accumulation of Marine Sponges in South China Sea Areas

2019 ◽  
Vol 8 (1) ◽  
pp. 63
Author(s):  
Huilong Ou ◽  
Mingyu Li ◽  
Shufei Wu ◽  
Linli Jia ◽  
Russell T. Hill ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Inorganic Phosphorus ◽  
Marine Sponges ◽  
Strongly Correlated ◽  
Mantel Tests ◽  
Low Concentrations ◽  
Enrichment Rate ◽  
Total Dna ◽  
Polyphosphate Accumulation ◽  
Sequence Similarities

Some sponges have been shown to accumulate abundant phosphorus in the form of polyphosphate (polyP) granules even in waters where phosphorus is present at low concentrations. But the polyP accumulation occurring in sponges and their symbiotic bacteria have been little studied. The amounts of polyP exhibited significant differences in twelve sponges from marine environments with high or low dissolved inorganic phosphorus (DIP) concentrations which were quantified by spectral analysis, even though in the same sponge genus, e.g., Mycale sp. or Callyspongia sp. PolyP enrichment rates of sponges in oligotrophic environments were far higher than those in eutrophic environments. Massive polyP granules were observed under confocal microscopy in samples from very low DIP environments. The composition of sponge symbiotic microbes was analyzed by high-throughput sequencing and the corresponding polyphosphate kinase (ppk) genes were detected. Sequence analysis revealed that in the low DIP environment, those sponges with higher polyP content and enrichment rates had relatively higher abundances of cyanobacteria. Mantel tests and canonical correspondence analysis (CCA) examined that the polyP enrichment rate was most strongly correlated with the structure of microbial communities, including genera Synechococcus, Rhodopirellula, Blastopirellula, and Rubripirellula. About 50% of ppk genes obtained from the total DNA of sponge holobionts, had above 80% amino acid sequence similarities to those sequences from Synechococcus. In general, it suggested that sponges employed differentiated strategies towards the use of phosphorus in different nutrient environments and the symbiotic Synechococcus could play a key role in accumulating polyP.

scholarly journals Denitrifying bacterial communities in surface-flow constructed wetlands during different seasons: characteristics and relationships with environment factors

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jia-ming Wei ◽  
Li-juan Cui ◽  
Wei Li ◽  
Yun-mei Ping ◽  
Wan Li
Keyword(s):  
Environmental Factors ◽  
High Throughput Sequencing ◽  
Bacterial Abundance ◽  
Flow Direction ◽  
Denitrifying Bacteria ◽  
Surface Flow ◽  
Strongly Correlated ◽  
Community Structures ◽  
Oxidation Reduction ◽  
Different Seasons

AbstractDenitrification is an important part of the nitrogen cycle and the key step to removal of nitrogen in surface-flow wetlands. In this study, we explored space–time analysis with high-throughput sequencing to elucidate the relationships between denitrifying bacteria community structures and environmental factors during different seasons. Our results showed that along the flow direction of different processing units, there were dynamic changes in physical and chemical indicators. The bacterial abundance indexes (ACEs) in May, August, and October were 686.8, 686.8, and 996.2, respectively, whereas the Shannon-Weiner indexes were 3.718, 4.303, and 4.432, respectively. Along the flow direction, the denitrifying bacterial abundance initially increased and then decreased subsequently during the same months, although diversity tended to increase. The abundance showed similar changes during the different months. Surface flow wetlands mainly contained the following denitrifying bacteria genus: unclassified Bacteria (37.12%), unclassified Proteobacteria (18.16%), Dechloromonas (16.21%), unranked environmental samples (12.51%), unclassified Betaproteobacteria (9.73%), unclassified Rhodocyclaceae (2.14%), and Rhodanobacter (1.51%). During different seasons, the same unit showed alternating changes, and during the same season, bacterial community structures were influenced by the second genus proportion in different processing units. ACEs were strongly correlated with temperature, dissolved oxygen, and pH. Bacterial diversity was strongly correlated with temperature, electrical conductivity, pH, and oxidation reduction potential. Denitrifying bacteria are greatly affected by environmental factors such as temperature and pH.

scholarly journals Clostridium chromiireducens sp. nov., isolated from Cr(VI)-contaminated soil

2011 ◽  
Vol 61 (11) ◽  
pp. 2626-2631 ◽  
Author(s):  
K. S. Inglett ◽  
H. S. Bae ◽  
H. C. Aldrich ◽  
K. Hatfield ◽  
A. V. Ogram
Keyword(s):  
Contaminated Soil ◽  
Clostridium Beijerinckii ◽  
Rrna Gene ◽  
Acid Fermentation ◽  
Mixed Acid ◽  
Morphological Studies ◽  
Group I ◽  
Low Concentrations ◽  
Low Levels ◽  
Sequence Similarities

A Cr(VI)-resistant, Gram-positive, spore-forming, obligate anaerobe, designated GCAF-1T, was isolated from chromium-contaminated soil by its ability to reduce Cr(VI) in low concentrations. Mixed acid fermentation during growth on glucose resulted in accumulation of acetate, butyrate, formate and lactate. Morphological studies indicated the presence of peritrichous flagella, pili and an S-layer. The major cellular fatty acids (>5 %) were C16 : 0, C14 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c), C18 : 1ω7c, C16 : 1ω9c, summed feature 4 (comprising iso-C17 : 1 I and/or anteiso-C17 : 1 B) and C18 : 1ω9c. The DNA G+C content of strain GCAF-1T was 30.7 mol%. Phylogenetic interference indicated that strain GCAF-1T clustered with group I of the genus Clostridium. Of strains within this cluster, strain GCAF-1T shared the highest 16S rRNA gene sequence similarities (98.1–98.9 %) with Clostridium beijerinckii DSM 791T, C. saccharobutylicum NCP 262T, C. saccharoperbutylacetonicum N1-4T, C. puniceum DSM 2619T and C. roseum DSM 51T. However, strain GCAF-1T could be clearly distinguished from its closest phylogenetic neighbours by low levels of DNA–DNA relatedness (<50 %) and some phenotypic features. Based on the evidence presented here, strain GCAF-1T ( = DSM 23318T  = KCTC 5935T) represents a novel species of the genus Clostridium, for which the name Clostridium chromiireducens sp. nov. is proposed.

scholarly journals DNA metabarcoding of fungal diversity in air and snow of Livingston Island, South Shetland Islands, Antarctica

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Luiz Henrique Rosa ◽  
Otávio Henrique Bezerra Pinto ◽  
Tina Šantl-Temkiv ◽  
Peter Convey ◽  
Micheline Carvalho-Silva ◽  
...  
Keyword(s):  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Rank Order ◽  
Mesh Size ◽  
Diversity Indices ◽  
South Shetland Islands ◽  
Livingston Island ◽  
Dna Metabarcoding ◽  
Air Sample ◽  
Total Dna

AbstractWe assessed fungal diversity present in air and freshly deposited snow samples obtained from Livingston Island, Antarctica, using DNA metabarcoding through high throughput sequencing (HTS). A total of 740 m3 of air were pumped through a 0.22 µm membrane. Snow obtained shortly after deposition was kept at room temperature and yielded 3.760 L of water, which was filtered using Sterivex membranes of 0.22 µm mesh size. The total DNA present was extracted and sequenced. We detected 171 fungal amplicon sequence variants (ASVs), 70 from the air and 142 from the snow. They were dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota and Mucoromycota. Pseudogymnoascus, Cladosporium, Mortierella and Penicillium sp. were the most dominant ASVs detected in the air in rank order. In snow, Cladosporium, Pseudogymnoascus, Penicillium, Meyerozyma, Lecidea, Malassezia, Hanseniaspora, Austroplaca, Mortierella, Rhodotorula, Penicillium, Thelebolus, Aspergillus, Poaceicola, Glarea and Lecanora were the dominant ASVs present. In general, the two fungal assemblages displayed high diversity, richness, and dominance indices, with the assemblage found in snow having the highest diversity indices. Of the total fungal ASVs detected, 29 were only present in the air sample and 101 in the snow sample, with only 41 present in both samples; however, when only the dominant taxa from both samples were compared none occurred only in the air and, among the rare portion, 26 taxa occurred in both air and snow. Application of HTS revealed the presence of a more diverse fungal community in the air and snow of Livingston Island in comparison with studies using traditional isolation methods. The assemblages were dominated by cold-adapted and cosmopolitan fungal taxa, including members of the genera Pseudogymnoascus, Malassezia and Rhodotorula, which include some taxa reported as opportunistic. Our results support the hypothesis that the presence of microbiota in the airspora indicates the possibility of dispersal around Antarctica in the air column. However, further aeromycology studies are required to understand the dynamics of fungal dispersal within and beyond Antarctica.

scholarly journals Effect of Exogenous Hormonal Stimulation on the Metabolic Partition between Plant Growth and Rubber Production of Hevea brasiliensis Clones According to the Class of Metabolic Activity in Cote d'ivoire

2021 ◽  
pp. 46-64
Author(s):  
Lehi Malidy Irénée ◽  
Konan Djezou ◽  
Okoma Koffi Mathurin ◽  
Yoboue Ange Naté ◽  
Konan Kouakou Séraphin ◽  
...  
Keyword(s):  
Metabolic Activity ◽  
Hevea Brasiliensis ◽  
Polynomial Function ◽  
Inorganic Phosphorus ◽  
Strongly Correlated ◽  
Hormonal Stimulation ◽  
Rubber Production ◽  
Good State ◽  
Growth Production ◽  
Low Sensitivity

Aims: In order to achieve a good and sustainable harvest of Hevea brasiliensis rubber, the effect of exogenous hormonal stimulation on the metabolic partition growth-production of clones according to the class of metabolic activity was made. Place and Duration of Study: The study was conducted for 9 years in the San-Pedro region in south-west Ivory Coast, precisely in the experimental industrial plantations of the former HEVEGO, now Southwestern Agricultural Civil Society Société (SCASO). Methodology and Results: The rubber trees were planted at a density of 510 trees/ha in a completely randomised system. They were bled in S/2 d4 and stimulated to 2.5% Etephon at annual frequencies of 0, 1, 2, 4, 6, 8, 13, 18, 26, 39 and 78. The parameters measured were rubber production, trunk circumference, sucrose content, inorganic phosphorus, thiol groups and dry notch rate. The results showed that productivity increased with the intensity of stimulation (58.96 - 68.49 g.a-1.s-1 ; 39.83 - 66.69 g.a-1.s-1) over the intervals [0.6] and [0.26] stimulations respectively in clones with active and slow metabolism. The circumference of the trunk was marked by a less pronounced decrease in growth in slow metabolizing clones (0.52%) with good protection of the laticigene system (R-SH : 0.815 mmol.l-1) and low sensitivity to dry notching (1.6). Whatever the classes of metabolic activity of the clones, the agrophysiological parameters were strongly correlated with each other by a degree 2 polynomial function. Conclusion: This polynomial function seems to reflect the existence of a good state of equilibrium between laticigenic metabolism and vegetative growth according to the class of metabolic activity of the Hevea brasiliensis clones.

scholarly journals Bioactive Metabolites of Marine Origin Have Unusual Effects on Model Membrane Systems

Marine Drugs ◽  
2020 ◽  
Vol 18 (2) ◽  
pp. 125 ◽  
Author(s):  
Martin Jakubec ◽  
Christian Totland ◽  
Frode Rise ◽  
Elahe Jafari Chamgordani ◽  
Britt Paulsen ◽  
...  
Keyword(s):  
Hexagonal Phase ◽  
Chemical Shift Anisotropy ◽  
Antimicrobial Activities ◽  
Marine Sponges ◽  
Model Systems ◽  
Bioactive Metabolites ◽  
Lamellar Phases ◽  
Low Concentrations ◽  
Simple Lipid ◽  
Future Work

Marine sponges and soft corals have yielded novel compounds with antineoplastic and antimicrobial activities. Their mechanisms of action are poorly understood, and in most cases, little relevant experimental evidence is available on this topic. In the present study, we investigated whether agelasine D (compound 1) and three agelasine analogs (compound 2–4) as well as malonganenone J (compound 5), affect the physical properties of a simple lipid model system, consisting of dioleoylphospahtidylcholine and dioleoylphosphatidylethanolamine. The data indicated that all the tested compounds increased stored curvature elastic stress, and therefore, tend to deform the bilayer which occurs without a reduction in the packing stress of the hexagonal phase. Furthermore, lower concentrations (1%) appear to have a more pronounced effect than higher ones (5–10%). For compounds 4 and 5, this effect is also reflected in phospholipid headgroup mobility assessed using 31P chemical shift anisotropy (CSA) values of the lamellar phases. Among the compounds tested, compound 4 stands out with respect to its effects on the membrane model systems, which matches its efficacy against a broad spectrum of pathogens. Future work that aims to increase the pharmacological usefulness of these compounds could benefit from taking into account the compound effects on the fluid lamellar phase at low concentrations.

scholarly journals Strategy for the Removal of Satellite Bacteria from the Cultivated Diatom

Diversity ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 382
Author(s):  
Yulia Zakharova ◽  
Artem Marchenkov ◽  
Nadezhda Volokitina ◽  
Aleksey Morozov ◽  
Yelena Likhoshway ◽  
...  
Keyword(s):  
Extracellular Polymeric Substances ◽  
High Throughput Sequencing ◽  
Single Cells ◽  
Axenic Culture ◽  
Blue Staining ◽  
Alcian Blue Staining ◽  
Bacterial Cells ◽  
Genetic Studies ◽  
Bacterial Dna ◽  
Total Dna

Multiple ecological and genetic studies of diatom algae require an axenic culture. However, algae-associated bacterial biofilms often form in diatom-produced mucus, both during creation of monoclonal cultures from single cells and during biomass growth, and they may be difficult to remove. In this work, we describe a protocol for removing associated bacteria from a monoclonal culture of Ulnaria danica isolated from Lake Baikal. The axenization strategy involves selecting the latent phase of diatom growth, multiple washes to remove extracellular polymeric substances and bacterial cells, filter deposition, and treatment with antibiotics that are not toxic for diatoms. The absence of bacteria during these stages was controlled by light microscopy with Alcian blue staining for mucus, epifluorescent microscopy with DAPI (4′,6-diamino-2-phenylindole) staining for bacterial DNA, and scanning electron microscopy of the diatom cell surface. High-throughput sequencing of a 16S rRNA fragment, amplified with universal bacterial primers, from total DNA of a final culture failed to detect any bacterial contamination, confirming successful axenization. A detailed comparative description of all stages of our protocol may prove useful in developing axenic cultures of other diatoms for various ecological and genetic studies.

scholarly journals Improving oligo-conjugated antibody signal in multimodal single-cell analysis

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Terkild B Buus ◽  
Alberto Herrera ◽  
Ellie Ivanova ◽  
Eleni Mimitou ◽  
Anthony Cheng ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Cell Number ◽  
Surface Proteins ◽  
Biological Information ◽  
High Background ◽  
Low Concentrations ◽  
High Concentrations ◽  
Insight Into

Simultaneous measurement of surface proteins and gene expression within single cells using oligo-conjugated antibodies offers high-resolution snapshots of complex cell populations. Signal from oligo-conjugated antibodies is quantified by high-throughput sequencing and is highly scalable and sensitive. We investigated the response of oligo-conjugated antibodies towards four variables: concentration, staining volume, cell number at staining, and tissue. We find that staining with recommended antibody concentrations causes unnecessarily high background and amount of antibody used can be drastically reduced without loss of biological information. Reducing staining volume only affects antibodies targeting abundant epitopes used at low concentrations and is counteracted by reducing cell numbers. Adjusting concentrations increases signal, lowers background, and reduces costs. Background signal can account for a major fraction of total sequencing and is primarily derived from antibodies used at high concentrations. This study provides new insight into titration response and background of oligo-conjugated antibodies and offers concrete guidelines to improve such panels.

scholarly journals Bacterial composition and inferring function profiles in the biofloc system rearing Litopenaeus vannamei postlarvae at a low salinity

2022 ◽  
Author(s):  
Hai-Hong Huang ◽  
Chao-Yun Li ◽  
Yan-Ju Lei ◽  
Wei-Qi Kuang ◽  
Wan-Sheng Zou ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Litopenaeus Vannamei ◽  
High Throughput Sequencing ◽  
Inorganic Nitrogen ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Low Salinity ◽  
Low Concentrations ◽  
Salinity Condition ◽  
Microbial Dna

This study aimed to investigate the bacterial composition and inferring function profiles in the biofloc system rearing Litopenaeus vannamei postlarvae (PL) at a low salinity condition. PL (~ stage 15) were stocked in four parallel tanks filled in water with a salinity of 5.0‰ at a density of 4000 individuals per m3 for a 28-days culture experiment, during which glucose was added as carbon source with a C:N of 20:1. At the end of experiment, water was sampled from each tank and pooled to extract microbial DNA for high-throughput sequencing of V3-V4 region of 16S rRNA gene. Results showed that the bacterial community at 28 d was dominated by phyla of Proteobacteria (45.8%), Bacteroidetes (21.1%), Planctomycetes (13.5%), Chlamydiae (10.3%) and Firmicutes (6.8%). A proportion of 81% inferring KEGG functions of this bacterial community associated with metabolism. Among functions relating to nitrogen metabolism, 48.5% were involved in the conversion of ammonia to glutamate, but the proportion of those involved in transformation among ammonia, nitrite and nitrate was 18.0% in total, inferring higher protein-synthesis but lower inorganic nitrogen-transformation capacities of the bacterial community. At the same time (28 d), high levels of total nitrogen (231.3±6.0 mg L-1) and biofloc (127.0±63.0 mL L-1), but low concentrations of ammonia (0.04±0.01 mg L-1), nitrite (0.2±0.1 mg L-1) and nitrate (12.9±2.5 mg L-1) were observed. The results supply a novel insight for understanding the function of bacterial community in the biofloc system nursing L. vannamei PL at a low salinity.

scholarly journals Consolida regalis Gray seed production as influenced by the habitat and crop plant in the western Podlasie region

2014 ◽  
Vol 66 (4) ◽  
pp. 165-172 ◽  
Author(s):  
Teresa Skrajna ◽  
Maria Ługowska ◽  
Janina Skrzyczyńska
Keyword(s):  
Seed Production ◽  
Soil Ph ◽  
Crop Plant ◽  
Available Phosphorus ◽  
Strongly Correlated ◽  
Production Potential ◽  
Nutrient Contents ◽  
Low Concentrations ◽  
Soil Complex ◽  
Inflorescence Structure

Studies were conducted in 2007–2009 in the Western Podlasie region to examine the seed production potential of <em>Consolida</em><em> </em><em>regalis</em><em> </em>under different habitat conditions. <em>Consolida</em><em> </em><em>regalis</em><em> </em>populations from 15 sites representing the habitat amplitude of this species were examined. Thirty morphologically different plants were sampled from each habitat and soil samples were taken to determine soil contents of available phosphorus (P), potassium (K) and magnesium (Mg) as well as pH. The results were statistically analysed. The seed production potential of the species studied was most strongly correlated with soil contents of magnesium (Mg), potassium (K), phosphorus (P) and soil pH. By contrast, the kind of crop plant and its cover were insignificant. Of the plant characteristics, plant height and traits associated with inflorescence structure had a significant influence on seed production potential. The populations with the greatest seed production potential produced an average of 1287 and 965 se- eds per plant. These populations were associated with the most fertile sites (good wheat soil complex) where the differences in seed production potential resulted from the nutrient contents and soil pH. By contrast, the least seeds were produced by plants growing on poor and acidic light soils. The average seed number per plant ranged from 42 to 83. Low concentrations of the nutrients examined were determined, with the soil content of magnesium being very low.

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