Bacterial Composition and Diversity in Deep-Sea Sediments from the Southern Colombian Caribbean Sea

Deep-sea sediments are considered an extreme environment due to high atmospheric pressure and low temperatures, harboring novel microorganisms. To explore marine bacterial diversity in the southern Colombian Caribbean Sea, this study used 16S ribosomal RNA (rRNA) gene sequencing to estimate bacterial composition and diversity of six samples collected at different depths (1681 to 2409 m) in two localities (CCS_A and CCS_B). We found 1842 operational taxonomic units (OTUs) assigned to bacteria. The most abundant phylum was Proteobacteria (54.74%), followed by Bacteroidetes (24.36%) and Firmicutes (9.48%). Actinobacteria and Chloroflexi were also identified, but their dominance varied between samples. At the class-level, Alphaproteobacteria was most abundant (28.4%), followed by Gammaproteobacteria (24.44%) and Flavobacteria (16.97%). The results demonstrated that some bacteria were common to all sample sites, whereas other bacteria were unique to specific samples. The dominant species was Erythrobacter citreus, followed by Gramella sp. Overall, we found that, in deeper marine sediments (e.g., locality CCS_B), the bacterial alpha diversity decreased while the dominance of several genera increased; moreover, for locality CCS_A, our results suggest that the bacterial diversity could be associated with total organic carbon content. We conclude that physicochemical properties (e.g., organic matter content) create a unique environment and play an important role in shaping bacterial communities and their diversity.

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Transition of Bacterial Diversity and Composition in Tongue Microbiota during the First Two Years of Life

mSphere ◽

10.1128/msphere.00187-19 ◽

2019 ◽

Vol 4 (3) ◽

Cited By ~ 1

Author(s):

Shinya Kageyama ◽

Mikari Asakawa ◽

Toru Takeshita ◽

Yukari Ihara ◽

Shunsuke Kanno ◽

...

Keyword(s):

Oral Cavity ◽

Bacterial Diversity ◽

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Oral Microbiota ◽

Bacterial Composition ◽

Content Type ◽

Operational Taxonomic Units ◽

Rrna Gene Sequencing

ABSTRACTNewborns are constantly exposed to various microbes from birth; hence, diverse commensal bacteria colonize the oral cavity. However, how or when these bacteria construct a complex and stable ecosystem remains unclear. This prospective cohort study examined the temporal changes in bacterial diversity and composition in tongue microbiota during infancy. We longitudinally collected a total of 464 tongue swab samples from 8 infants (age of <6 months at baseline) for approximately 2 years. We also collected samples from 32 children (aged 0 to 2 years) and 73 adults (aged 20 to 29 years) cross-sectionally as control groups. Bacterial diversities and compositions were determined by 16S rRNA gene sequencing. The tongue bacterial diversity in infancy, measured as the number of observed operational taxonomic units (OTUs), rapidly increased and nearly reached the same level as that in adults by around 80 weeks. The overall tongue bacterial composition in the transitional phase, 80 to 120 weeks, was more similar to that of adults than to that of the early exponential phase (EEP), 10 to 29 weeks, according to analysis of similarities. Dominant OTUs in the EEP corresponding toStreptococcus perorisandStreptococcus lactariusexponentially decreased immediately after EEP, around 30 to 49 weeks, whereas several OTUs corresponding toGranulicatella adiacens,Actinomyces odontolyticus, andFusobacterium periodonticumreciprocally increased during the same period. These results suggest that a drastic compositional shift of tongue microbiota occurs before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years.IMPORTANCEEvaluating the development of oral microbiota during infancy is important for understanding the subsequent colonization of bacterial species and the process of formation of mature microbiota in the oral cavity. We examined tongue microbiota longitudinally collected from 8 infants and found that drastic compositional shifts in tongue microbiota occur before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years. These results may be helpful for preventing the development of various diseases associated with oral microbiota throughout life.

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Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau

Antonie van Leeuwenhoek ◽

10.1007/s10482-020-01384-8 ◽

2020 ◽

Vol 113 (5) ◽

pp. 707-717 ◽

Cited By ~ 2

Author(s):

Luciano Lopes Queiroz ◽

Amanda Gonçalves Bendia ◽

Rubens Tadeu Delgado Duarte ◽

Diego Assis das Graças ◽

Artur Luiz da Costa da Silva ◽

...

Keyword(s):

Bacterial Diversity ◽

Deep Sea ◽

Sao Paulo ◽

São Paulo ◽

Deep Sea Sediments

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Organic matter content controls the N and P degradation process on biogeochemical interfaces: A micro-ecosystem scale study based on SoilChips-XPS-Zymography integrated technique in paddy soils

10.5194/egusphere-egu2020-2963 ◽

2020 ◽

Author(s):

Liang Wei

Keyword(s):

Organic Matter ◽

Dissolved Organic Matter ◽

Photoelectron Spectroscopy ◽

Organic Matter Content ◽

Degradation Process ◽

Matter Content ◽

Microbial Production ◽

Paddy Soils ◽

Rrna Gene ◽

Degradation Processes

<p>The biogeochemical interfaces are hotspots for organic matter (OM) transformation. However, direct and continuouxiacis tracing of OM transformations and N and P degradation processes are lacking due to the heterogeneous and opaque nature of soil microenvironment. To investigate these processes, a new soil microarray technology (SoilChips) was developed and used. Homogeneous 2-mm-diameter SoilChips were constructed by depositing a dispersed paddy soils with high and low soil organic carbon (SOC) content. A horizon suspension on a patterned glass. Dissolved organic matter from the original soil was added on the SoilChips to mimic biogeochemical processes on interfaces. The chemical composition of biogeochemical interfaces were evaluated via X-ray photoelectron spectroscopy (XPS) and the two-dimensional distribution of enzyme activities in SoilChips were evaluated by zymography. Over 30 days, soil with high SOC content increases microbial nutrition (N and P) requirements than soil with low SOC evidenced by higher hotspots of &#946;-1,4-N-acetaminophen glucosidase, and acid phosphomonoesterases and higher 16S rRNA gene copies. The degree of humification in dissolved organic matter (DOM) was higher and the bioavailability of DOM was poorer in soil with high SOC than soil with low SOC. The poorest bioavailability of DOM was detected at the end of incubation in soil with high SOC. Molecular modeling of OM composition showed that low SOC mainly facilitated the microbial production of glucans but high SOC mainly facilitated the microbial production of proteins. We demonstrated that SOC content or DOM availability for microorganisms modifies the specific OM molecular processing and N and P degradation processes, thereby providing a direct insight into biogeochemical transformation of OM at micro-scale.</p>

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Organic carbon determination in histosols and soil horizons with high organic matter content from Brazil

Scientia Agricola ◽

10.1590/s0103-90162006000200012 ◽

2006 ◽

Vol 63 (2) ◽

pp. 187-193 ◽

Cited By ~ 15

Author(s):

Marcos Gervasio Pereira ◽

Gustavo Souza Valladares ◽

Lúcia Helena Cunha dos Anjos ◽

Vinícius de Melo Benites ◽

Ademar Espíndula Jr. ◽

...

Keyword(s):

Organic Matter ◽

Organic Carbon ◽

Organic Matter Content ◽

Analysis Data ◽

Matter Content ◽

Organic Soils ◽

Organic Carbon Content ◽

Muffle Furnace ◽

Soil Taxonomy ◽

High Organic Carbon Content

Soil taxonomy systems distinguish mineral soils from organic soils based on the amount of soil organic carbon. Procedures adopted in soil surveys for organic carbon measurement are therefore of major importance to classify the soils, and to correlate their properties with data from other studies. To evaluate different methods for measuring organic carbon and organic matter content in Histosols and soils with histic horizons, from different regions of Brazil, 53 soil samples were comparatively analyzed by the methods of Walkley & Black (modified), Embrapa, Yeomans & Bremner, modified Yeomans & Bremner, muffle furnace, and CHN. The modified Walkley & Black (C-W & B md) and the combustion of organic matter in the muffle furnace (OM-Muffle) were the most suitable for the samples with high organic carbon content. Based on regression analysis data, the OM-muffle may be estimated from C-W & B md by applying a factor that ranges from 2.00 to 2.19 with 95% of probability. The factor 2.10, the average value, is suggested to convert results obtained by these methods.

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Combining Multiple Markers in Environmental DNA Metabarcoding to Assess Deep-Sea Benthic Biodiversity

Frontiers in Marine Science ◽

10.3389/fmars.2021.684955 ◽

2021 ◽

Vol 8 ◽

Author(s):

Jun Liu ◽

Haibin Zhang

Keyword(s):

Deep Sea ◽

Okinawa Trough ◽

Environmental Dna ◽

Rrna Gene ◽

28S Rrna ◽

Eukaryotic Diversity ◽

The Okinawa Trough ◽

Marine Diversity ◽

Deep Sea Sediments ◽

Reference Databases

Environmental DNA (eDNA) metabarcoding is an emerging tool to estimate diversity by combining DNA from the environmental samples and the high-throughput sequencing. Despite its wide use in estimating eukaryotic diversity, many factors may bias the results. Maker choice and reference databases are among the key issues in metabarcoding analyses. In the present study, we compared the performance of a novel 28S rRNA gene marker designed in this study and two commonly used 18S rRNA gene markers (V1-2 and V9) in estimating the eukaryotic diversity in the deep-sea sediments. The metabarcoding analyses based on the sediment surveys of the Okinawa Trough found that more eukaryotic taxa were discovered by 18S V9 than 28S and 18S V1-2, and that 18S V9 also performed better in metazoan recovery than the other two markers. Although a broad range of taxa were detected by the three metabarcoding markers, only a small proportion of taxa were shared between them even at the phylum level. The non-metric multidimensional scaling (NMDS) analysis also supported that communities detected by the three markers were distinct from each other. In addition, different communities were resolved by different reference databases (NCBI nt vs. SILVA) for the two 18S markers. Combining the three markers, annelids were found to be the most abundant (44.9%) and diverse [179 operational taxonomic units (OTUs)] metazoan group in the sediments of the Okinawa Trough. Therefore, multiple independent markers are recommended to be used in metabarcoding analyses during marine diversity surveys, especially for the poorly understood deep-sea sediments.

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The color of refractory organic carbon

BSGF - Earth Sciences Bulletin ◽

10.1051/bsgf/2018008 ◽

2018 ◽

Vol 189 (2) ◽

pp. 9 ◽

Cited By ~ 1

Author(s):

Maxime Debret ◽

Yoann Copard ◽

Antonin Van Exem ◽

Geneviève Bessereau ◽

Frank Haeseler ◽

...

Keyword(s):

Organic Matter ◽

Organic Carbon ◽

Carbon Content ◽

Anthropogenic Activities ◽

Organic Matter Content ◽

Matter Content ◽

Mineral Matter ◽

Organic Carbon Content ◽

Fast Method ◽

Wide Range

Organic matter studies find an echo within different topics such as biogeochemical cycles, processes occurring in continental surfaces, anthropogenic activities, climate science, earth and planetary sciences, etc. Today’s challenges include finding and developing the most appropriate method(s) supporting the differentiation and characterisation of various types of recalcitrant organic matter in modern environments. In this study, we focus on combustion residues and coals as these two types of organic matter contain a significant amount of so-called recalcitrant organic carbon (black carbon and fossil organic carbon). Both these materials are ubiquitous, broadly stem from the same living organisms and have similar polyaromatic structures. In this respect, we tested a spectrophotometry method, classically used for sedimentology, as a very fast method for preliminary investigations. Analyses were performed with a wide range of standards and referenced samples. The results discriminate three different spectral signatures related to the degree of transformation of organic matter related to the degree of aromaticity (i.e. carbonisation). Using calibration curves, total organic carbon content can be estimated in experimental mixes with mineral matter and in a real context using subsurface sample (Gironville 101 borehole, Paris Basin, France). This method has particularly high sensitivity to very low organic matter content and is shown to be promising for a rapid evaluation of the organic carbon content.

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Impacts de l’agriculture de conservation sur les propriétés et la productivité des vertisols du Maroc Central

Afrika Focus ◽

10.21825/af.v25i2.4957 ◽

2012 ◽

Vol 25 (2) ◽

Author(s):

Rachid Moussadek

Keyword(s):

Crop Yields ◽

Management Practice ◽

Soil Water Potential ◽

Organic Matter Content ◽

Soil Nutrient ◽

Crop Productivity ◽

Matter Content ◽

Water Infiltration ◽

Organic Carbon Content ◽

Nutrient Pool

In Morocco, intensive agriculture with deep tillage and soil inversion caused rapid soil structure deterioration with loss of soil organic matter content. This practice leads to a decrease in soil fertility, a degradation of the soil physical properties and a reduction of crop yields in different soil types, such as Vertisols. In fact, Vertisols (or Tirs as vernacular name) are among the most productive soils in Morocco, but they are also susceptible to compaction and reduced water infiltration due to intensive tillage. No-tillage (NT) is commonly promoted as a management practice capable of offsetting soil carbon depletion, improving aggregation, enriching the soil nutrient pool and enhancing crop productivity in many parts of the world. However, the influence of the NT system as compared to the conventional tillage (CT) system on physical, chemical and hydrodynamic soil properties was not yet well studied in the semi-arid environment of Morocco where rainfall ranges from 350 to 600 mm. This research focused mainly on those parameters with important agronomical or environmental impact: bulk density (Db), soil strength assessed using cone index (CI), hydraulic conductivity (K), sorptivity (S), soil water potential (SWP), soil organic carbon content or stock (SOCc or SOCs), runoff, soil loss, soil CO2 emission and crop yield.

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Bacterial Diversity in Deep-Sea Sediments from Afanasy Nikitin Seamount, Equatorial Indian Ocean

Geomicrobiology Journal ◽

10.1080/01490451.2014.918214 ◽

2014 ◽

Vol 31 (10) ◽

pp. 942-949 ◽

Cited By ~ 6

Author(s):

Rakhee Khandeparker ◽

Ram Murti Meena ◽

Deepti Deobagkar

Keyword(s):

Indian Ocean ◽

Bacterial Diversity ◽

Deep Sea ◽

Equatorial Indian Ocean ◽

Deep Sea Sediments

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Upper Jurassic–Lower Cretaceous Source Rocks in the North of Western Siberia: Comprehensive Geochemical Characterization and Reconstruction of Paleo-Sedimentation Conditions

Geosciences ◽

10.3390/geosciences11080320 ◽

2021 ◽

Vol 11 (8) ◽

pp. 320

Author(s):

Evgeniya Leushina ◽

Timur Bulatov ◽

Elena Kozlova ◽

Ivan Panchenko ◽

Andrey Voropaev ◽

...

Keyword(s):

Organic Matter ◽

Lower Cretaceous ◽

Organic Matter Content ◽

Upper Jurassic ◽

Matter Content ◽

Source Rocks ◽

Organic Carbon Content ◽

Sea Level Changes ◽

The North ◽

Terrigenous Sedimentation

The present work is devoted to geochemical studies of the Bazhenov Formation in the north of the West Siberian Petroleum Basin. The object is the Upper Jurassic–Lower Cretaceous section, characterized by significant variations in total organic carbon content and petroleum generation potential of organic matter at the beginning of the oil window. The manuscript presents the integration of isotopic and geochemical analyses aimed at the evaluation of the genesis of the rocks in the peripheral part of the Bazhenov Sea and reconstruction of paleoenvironments that controlled the accumulation of organic matter in sediments, its composition and diagenetic alterations. According to the obtained data, the sediments were accumulated under marine conditions with a generally moderate and periodically increasing terrigenous influx. The variations in organic matter composition are determined by redox conditions and terrigenous input which correlate with the eustatic sea level changes during transgressive/regressive cycles and activation of currents. Transgression is associated with an intensive accumulation of organic matter under anoxic to euxinic conditions and insignificant influence of terrigenous sources, resulting in the formation of rocks with oil-generating properties. During the regression periods, the terrigenous sedimentation increased along with the dissolved oxygen concentration, and deposits with low organic matter content and gas-generating properties were formed.

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Degradation of atrazine and bromacil in two forestry waste products

Scientific Reports ◽

10.1038/s41598-021-83052-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Trevor K. James ◽

Hossein Ghanizadeh ◽

Kerry C. Harrington ◽

Nanthi S. Bolan

Keyword(s):

Organic Matter ◽

Organic Matter Content ◽

Matter Content ◽

Organic Media ◽

Organic Carbon Content ◽

Waste Products ◽

Herbicide Degradation ◽

Temperature Regimes ◽

Degradation Rates ◽

Subsequent Degradation

AbstractThe persistence and degradation of two common herbicides, atrazine and bromacil in two organic media, wood pulp and sawdust were compared with two soils. The hypothesis tested was that herbicide degradation will be faster in high organic matter media compared to soil. Degradation of two herbicides was carried out in four different temperature regimes and in sterilised media. The degradation half-life (t½) was determined under above-mentioned conditions then compared to degradation in soil. The degradation as quantified by t½ of the herbicides was generally longer in both organic media. Although microbial degradation was an important factor in the mineralisation of these herbicides, overall, the pH of the media had a more profound effect on the desorption and subsequent degradation rate than the organic carbon content. The results of this study revealed that the hypothesis was only partially correct as organic matter content per se did not strongly relate to degradation rates which were mainly governed by pH and microbial activity.

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