scholarly journals Preliminary assessment of methanogenic microbial communities in marine caves of Zakynthos Island (Ionian Sea, Greece)

2018 ◽  
pp. 284
Author(s):  
PARASKEVI POLYMENAKOU ◽  
MANOLIS MANDALAKIS ◽  
THANOS DAILIANIS ◽  
CHARALAMPOS DIMITRIADIS ◽  
MATEJ MEDVECKY ◽  
...  
Keyword(s):  
Room Temperature ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Limited Information ◽  
Preliminary Assessment ◽  
Microbial Life ◽  
Incertae Sedis ◽  
Marine Caves ◽  
Different Types ◽  
Anaerobic Microbial Community

Mediterranean marine caves remain largely unexplored, while particularly limited information is available about the microbial life existing in these unique environments. The present study is a preliminary assessment of the composition of the active anaerobic microbial community colonizing the walls of newly explored systems of underwater caves and small cavities in Zakynthos Island. The interior of these caves is densely coated with egg-shaped, foam-shaped and filamentous biological structures that are characterised by a strong odor of hydrogen sulfide gas. A total of twelve structures scrapped from cave rocks were subjected to anaerobic cultivation for up to 208 days. Strong to moderate methanogenesis was observed in two different types of egg-shaped structures and one foam-like structure. Interestingly, this was observed in experiments that were performed at room temperature (i.e. 25oC) which is substantially lower than those typically considered optimum for methane production (e.g. 35oC). Analysis of the 16S rRNA genes revealed a clear dominance of archaea and bacteria closely related to known methane producers and sulfate reducers, including members of the families Methanomicrobiaceae, Desulfobulbaceae, Desulfobacteraceae, Desulfuromonaceae, Campylobacteraceae, Marinifilaceae, Clostridiaceae, Incertae Sedis – Family I & II. These results show that Mediterranean marine caves can host members of archaea and bacteria with potential biotechnological interest that deserve further investigation.

scholarly journals Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks

2021 ◽  
Author(s):  
Ömer K. Coskun ◽  
Aurèle Vuillemin ◽  
Florence Schubotz ◽  
Frieder Klein ◽  
Susanna E. Sichel ◽  
...  
Keyword(s):  
Subduction Zones ◽  
Carbon Assimilation ◽  
Oceanic Lithosphere ◽  
Stable Isotope Probing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ultramafic Rocks ◽  
Microbial Life ◽  
Order Of Magnitude ◽  
Mid Atlantic Ridge

AbstractThermodynamic models predict that H2 is energetically favorable for seafloor microbial life, but how H2 affects anabolic processes in seafloor-associated communities is poorly understood. Here, we used quantitative 13C DNA stable isotope probing (qSIP) to quantify the effect of H2 on carbon assimilation by microbial taxa synthesizing 13C-labeled DNA that are associated with partially serpentinized peridotite rocks from the equatorial Mid-Atlantic Ridge. The rock-hosted seafloor community was an order of magnitude more diverse compared to the seawater community directly above the rocks. With added H2, peridotite-associated taxa increased assimilation of 13C-bicarbonate and 13C-acetate into 16S rRNA genes of operational taxonomic units by 146% (±29%) and 55% (±34%), respectively, which correlated with enrichment of H2-oxidizing NiFe-hydrogenases encoded in peridotite-associated metagenomes. The effect of H2 on anabolism was phylogenetically organized, with taxa affiliated with Atribacteria, Nitrospira, and Thaumarchaeota exhibiting the most significant increases in 13C-substrate assimilation in the presence of H2. In SIP incubations with added H2, an order of magnitude higher number of peridotite rock-associated taxa assimilated 13C-bicarbonate, 13C-acetate, and 13C-formate compared to taxa that were not associated with peridotites. Collectively, these findings indicate that the unique geochemical nature of the peridotite-hosted ecosystem has selected for H2-metabolizing, rock-associated taxa that can increase anabolism under high H2 concentrations. Because ultramafic rocks are widespread in slow-, and ultraslow-spreading oceanic lithosphere, continental margins, and subduction zones where H2 is formed in copious amounts, the link between H2 and carbon assimilation demonstrated here may be widespread within these geological settings.

scholarly journals Phylogenetic Diversity and Metabolic Potential Revealed in a Glacier Ice Metagenome

2009 ◽  
Vol 75 (23) ◽  
pp. 7519-7526 ◽  
Author(s):  
Carola Simon ◽  
Arnim Wiezer ◽  
Axel W. Strittmatter ◽  
Rolf Daniel
Keyword(s):  
16S Rrna ◽  
Phylogenetic Diversity ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Metabolic Potential ◽  
Data Set ◽  
Glacial Ice ◽  
Microbial Life ◽  
Derived Data

ABSTRACT The largest part of the Earth's microbial biomass is stored in cold environments, which represent almost untapped reservoirs of novel species, processes, and genes. In this study, the first metagenomic survey of the metabolic potential and phylogenetic diversity of a microbial assemblage present in glacial ice is presented. DNA was isolated from glacial ice of the Northern Schneeferner, Germany. Pyrosequencing of this DNA yielded 1,076,539 reads (239.7 Mbp). The phylogenetic composition of the prokaryotic community was assessed by evaluation of a pyrosequencing-derived data set and sequencing of 16S rRNA genes. The Proteobacteria (mainly Betaproteobacteria), Bacteroidetes, and Actinobacteria were the predominant phylogenetic groups. In addition, isolation of psychrophilic microorganisms was performed, and 13 different bacterial isolates were recovered. Analysis of the 16S rRNA gene sequences of the isolates revealed that all were affiliated to the predominant groups. As expected for microorganisms residing in a low-nutrient environment, a high metabolic versatility with respect to degradation of organic substrates was detected by analysis of the pyrosequencing-derived data set. The presence of autotrophic microorganisms was indicated by identification of genes typical for different ways of carbon fixation. In accordance with the results of the phylogenetic studies, in which mainly aerobic and facultative aerobic bacteria were detected, genes typical for central metabolism of aerobes were found. Nevertheless, the capability of growth under anaerobic conditions was indicated by genes involved in dissimilatory nitrate/nitrite reduction. Numerous characteristics for metabolic adaptations associated with a psychrophilic lifestyle, such as formation of cryoprotectants and maintenance of membrane fluidity by the incorporation of unsaturated fatty acids, were detected. Thus, analysis of the glacial metagenome provided insights into the microbial life in frozen habitats on Earth, thereby possibly shedding light onto microbial life in analogous extraterrestrial environments.

scholarly journals Presence of orange tubercles does not always indicate accelerated low water corrosion

2019 ◽  
Author(s):  
Hoang C. Phan ◽  
Scott A. Wade ◽  
Linda L. Blackall
Keyword(s):  
Microbial Communities ◽  
Steel Sheet ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Accelerated Corrosion ◽  
Sulfate Reducing ◽  
Metallurgical Analysis ◽  
Different Types ◽  
Steel Surfaces ◽  
Reducing Bacteria

ABSTRACTThe rapid degradation of marine infrastructure at the low tide level due to accelerated low water corrosion (ALWC) is a problem encountered worldwide. Despite this, there is limited understanding of the microbial communities involved in this process. We obtained samples of the orange-coloured tubercles commonly associated with ALWC from two different types of steel sheet piling, located adjacent to each other but with different levels of localised corrosion, at a seaside harbour. The microbial communities from the outer and inner layers of the orange tubercles, and from adjacent seawater, were studied by pure culture isolation and metabarcoding of the 16S rRNA genes. A collection of 119 bacterial isolates was obtained from one orange tubercle sample, using a range of media with anaerobic and aerobic conditions. The metabarcoding results showed that sulfur and iron oxidisers were more abundant on the outer section of the orange tubercles compared to the inner layers, where Deltaproteobacteria (which includes many sulfate reducers) were more abundant. The microbial communities varied significantly between the inner and outer layers of the orange tubercles and also with the seawater, but overall did not differ significantly between the two steel sheet types. Metallurgical analysis found differences in composition, grain size, ferrite-pearlite ratio and the extent of inclusions present between the two steel types investigated.IMPORTANCEThe presence of orange tubercles on marine steel pilings is often used as an indication that accelerated low water corrosion is taking place. We studied the microbial communities in attached orange tubercles on two closely located sheet pilings that were of different steel types. The attached orange tubercles were visually similar, but the extent of underlying corrosion on the different steel surfaces were substantially different. No clear difference was found between the microbial communities present on the two different types of sheet piling. However, there were clear differences in the microbial communities in the corrosion layers of tubercles, which were also different to the microbes present in adjacent seawater. The overall results suggest that the presence of orange tubercles, a single measurement of water quality, or the detection of certain general types of microbes (e.g. sulfate reducing bacteria) should not be taken alone as definitive indications of accelerated corrosion.

scholarly journals Microbial Communities of Orange Tubercles in Accelerated Low-Water Corrosion

2020 ◽  
Vol 86 (13) ◽  
Author(s):  
Hoang C. Phan ◽  
Scott A. Wade ◽  
Linda L. Blackall
Keyword(s):  
Microbial Communities ◽  
Steel Sheet ◽  
Localized Corrosion ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Accelerated Corrosion ◽  
Content Type ◽  
Sulfate Reducing ◽  
Different Types ◽  
Different Levels

ABSTRACT The rapid degradation of marine infrastructure at the low tide level due to accelerated low-water corrosion (ALWC) is a problem encountered worldwide. Despite this, there is limited understanding of the microbial communities involved in this process. We obtained samples of the orange-colored tubercles commonly associated with ALWC from two different types of steel sheet piling, located adjacent to each other but with different levels of localized corrosion, at a seaside harbor. The microbial communities from the outer and inner layers of the orange tubercles and from adjacent seawater were studied by pure culture isolation and metabarcoding of the 16S rRNA genes. A collection of 119 bacterial isolates was obtained from one orange tubercle sample, using a range of media in anaerobic and aerobic conditions. The metabarcoding results showed that sulfur and iron oxidizers were more abundant on the outer sections of the orange tubercles compared to the inner layers, where Deltaproteobacteria (which include many sulfate reducers) were more abundant. The microbial communities varied significantly between the inner and outer layers of the orange tubercles and also with the seawater but overall did not differ significantly between the two steel sheet types. Hence, we saw similar microbial communities in orange tubercles present, but different levels of localized corrosion, for two different types of colocated steel sheet piling. Metallurgical analysis found differences in composition, grain size, ferrite-pearlite ratio, and the extent of inclusions present between the two steel types investigated. IMPORTANCE The presence of orange tubercles on marine steel pilings is often used as an indication that accelerated low-water corrosion is taking place. We studied the microbial communities in attached orange tubercles on two closely located sheet pilings that were of different steel types. The attached orange tubercles were visually similar, but the extents of underlying corrosion on the different steel surfaces were substantially different. No clear difference was found between the microbial communities present on the two different types of sheet piling. However, there were clear differences in the microbial communities in the corrosion layers of tubercles, which were also different from the microbes present in adjacent seawater. The overall results suggest that the presence of orange tubercles, a single measurement of water quality, or the detection of certain general types of microbes (e.g., sulfate-reducing bacteria) should not be taken alone as definitive indications of accelerated corrosion.

scholarly journals Diversity of NC10 Bacteria and ANME-2d Archaea in Sediments of Fault Zones at Lake Baikal

Diversity ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 10
Author(s):  
Anna Lomakina ◽  
Tatyana Pogodaeva ◽  
Gennady Kalmychkov ◽  
Svetlana Chernitsyna ◽  
Tamara Zemskaya
Keyword(s):  
Lake Baikal ◽  
High Throughput Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Pcr Analysis ◽  
Anaerobic Oxidation Of Methane ◽  
Oxidation Of Methane ◽  
Different Types ◽  
Freshwater Reservoir ◽  
Deep Sediments

Anaerobic oxidation of methane (AOM) reduces methane emissions from marine ecosystems, but we know little about AOM in freshwater reservoirs. Lake Baikal is the world’s only freshwater reservoir where gas hydrates (GH) are found. Despite that AOM has been demonstrated in deep sediments of Lake Baikal did not reveal methane-oxidizing archaea ANME1, 2, or 3, which are responsible for AOM in marine sediments. A search for representatives Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria (NC10) and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like archaea (ANME-2d) has been carried out in the different types of Lake Baikal methane enriched sediments. We used different molecular biology methods including high-throughput sequencing and PCR analysis, using 16S rRNA genes as well as different functional genes of AOM (mcrA and pmoA). We found diverse M. oxyfera-like bacteria and M. nitroreducens-like archaea in various geological structures in Lake Baikal (methane seep and mud volcano), which were different from the composition of the discharged fluid. We also considered possible electron acceptors for this process in the sediments of Lake Baikal.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

scholarly journals Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 40
Author(s):  
Liang Cui ◽  
Bitong Zhu ◽  
Xiaobo Zhang ◽  
Zhuhua Chan ◽  
Chungui Zhao ◽  
...  
Keyword(s):  
Water Quality ◽  
16S Rrna ◽  
Relative Abundance ◽  
Animal Health ◽  
Denitrifying Bacteria ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Analysis ◽  
Shrimp Culture

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

scholarly journals Coordination of microbe–host homeostasis by crosstalk with plant innate immunity

Nature Plants ◽  
2021 ◽  
Author(s):  
Ka-Wai Ma ◽  
Yulong Niu ◽  
Yong Jia ◽  
Jana Ordon ◽  
Charles Copeland ◽  
...  
Keyword(s):  
Growth Inhibition ◽  
Amplicon Sequencing ◽  
Host Susceptibility ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Root Growth Inhibition ◽  
Natural Soil ◽  
Molecular Pattern ◽  
Immune Related Genes ◽  
Molecular Patterns

AbstractPlants grown in natural soil are colonized by phylogenetically structured communities of microbes known as the microbiota. Individual microbes can activate microbe-associated molecular pattern (MAMP)-triggered immunity (MTI), which limits pathogen proliferation but curtails plant growth, a phenomenon known as the growth–defence trade-off. Here, we report that, in monoassociations, 41% (62 out of 151) of taxonomically diverse root bacterial commensals suppress Arabidopsis thaliana root growth inhibition (RGI) triggered by immune-stimulating MAMPs or damage-associated molecular patterns. Amplicon sequencing of bacterial 16S rRNA genes reveals that immune activation alters the profile of synthetic communities (SynComs) comprising RGI-non-suppressive strains, whereas the presence of RGI-suppressive strains attenuates this effect. Root colonization by SynComs with different complexities and RGI-suppressive activities alters the expression of 174 core host genes, with functions related to root development and nutrient transport. Furthermore, RGI-suppressive SynComs specifically downregulate a subset of immune-related genes. Precolonization of plants with RGI-suppressive SynComs, or mutation of one commensal-downregulated transcription factor, MYB15, renders the plants more susceptible to opportunistic Pseudomonas pathogens. Our results suggest that RGI-non-suppressive and RGI-suppressive root commensals modulate host susceptibility to pathogens by either eliciting or dampening MTI responses, respectively. This interplay buffers the plant immune system against pathogen perturbation and defence-associated growth inhibition, ultimately leading to commensal–host homeostasis.

scholarly journals Comparison of oral microbiome profiles in 18-month-old infants and their parents

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ryutaro Jo ◽  
Kazuma Yama ◽  
Yuto Aita ◽  
Kota Tsutsumi ◽  
Chikako Ishihara ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Dental Caries ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Commensal Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Deciduous Dentition ◽  
The Difference ◽  
Generation Sequencing

AbstractThe onset and progress of dental caries and periodontal disease is associated with the oral microbiome. Therefore, it is important to understand the factors that influence oral microbiome formation. One of the factors that influence oral microbiome formation is the transmission of oral bacteria from parents. However, it remains unclear when the transmission begins, and the difference in contributions of father and mother. Here, we focused on the oral microbiome of 18-month-old infants, at which age deciduous dentition is formed and the oral microbiome is likely to become stable, with that of their parents. We collected saliva from forty 18-month-old infants and their parents and compared the diversity and composition of the microbiome using next-generation sequencing of 16S rRNA genes. The results showed that microbial diversity in infants was significantly lower than that in parents and composition of microbiome were significantly different between infants and parents. Meanwhile, the microbiome of the infants was more similar to that of their mothers than unrelated adults. The bacteria highly shared between infants and parents included not only commensal bacteria but also disease related bacteria. These results suggested that the oral microbiome of the parents influences that of their children aged < 18 months.

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