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

2019 ◽  
Author(s):  
Luciano Lopes Queiroz ◽  
Amanda Gonçalves Bendia ◽  
Rubens Tadeu Delgado Duarte ◽  
Diego Assis das Graças ◽  
Artur Luiz da Costa da Silva ◽  
...  
Keyword(s):  
Deep Sea ◽  
Bacterial Communities ◽  
Sao Paulo ◽  
Rrna Gene ◽  
São Paulo ◽  
Operational Taxonomic Units ◽  
Uncultured Bacteria ◽  
Abundant Otus ◽  
Sediment Layers ◽  
Next Generation Sequencing Ngs

AbstractHere we investigated the diversity of bacterial communities from deep-sea surface sediments under influence of asphalt seeps at the Sao Paulo Plateau using next-generation sequencing (NGS) method. Sampling was performed at North São Paulo Plateau using the human occupied vehicle Shinkai 6500 and her support vessel Yokosuka. The microbial diversity was studied at two surficial sediment layers (0-1 and 1-4 cm) of five samples collected in cores in water depths ranging from 2,456-2,728 m. Bacterial communities were studied through sequencing of 16S rRNA gene on the Ion Torrent platform and clustered in operational taxonomic units. We observed high diversity of bacterial sediment communities as previously described by other studies. When we considered community composition, the most abundant classes were Alphaprotebacteria (27.7%), Acidimicrobiia (20%), Gammaproteobacteria (11.3%) and Deltaproteobacteria (6.6%). Most abundant OTUs at family level were from two uncultured bacteria from Actinomarinales (5.95%) and Kiloniellaceae (3.17%). The unexpected high abundance of Alphaproteobacteria and Acidimicrobiia in our deep-sea microbial communities may be related to the presence of asphalt seep at North São Paulo Plateau, since these bacterial classes contain bacteria that possess the capability of metabolizing hydrocarbon compounds.

scholarly journals The Bacterial Community Associated with the Amarillo Zamorano Maize (Zea mays) Landrace Silage Process

2020 ◽  
Vol 8 (10) ◽  
pp. 1503
Author(s):  
Humberto Ramírez-Vega ◽  
Ramón I. Arteaga-Garibay ◽  
Otoniel Maya-Lucas ◽  
Victor M. Gómez-Rodríguez ◽  
Ismael F. Chávez-Díaz ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Rrna Gene ◽  
Local Conditions ◽  
Operational Taxonomic Units ◽  
Maize Seeds ◽  
Hypervariable Regions ◽  
Silage Fermentation ◽  
Silage Process ◽  
Next Generation Sequencing Ngs

Maize silage is used in the diet of dairy cows, with suitable results in milk yield. In this study, the composition and diversity of the bacterial communities of the silage process of Amarillo Zamorano (AZ) Mexican maize landrace with relation to the Antilope (A) commercial hybrid are described. From both types of maize, seeds were sown in experimental plots, plants harvested at the reproductive stage, chopped, and packed in laboratory micro-silos. Physicochemical parameters were evaluated, and DNA was extracted from the juice in the micro-silos. The bacterial communities were analyzed by next-generation sequencing (NGS) of seven hypervariable regions of the 16S rRNA gene. The composition of both bacterial communities was dominated by Lactobacillales and Enterobacteriales, Lactobacillales mainly in A silage and Enterobacteriales in AZ silage; as well, the core bacterial community of both silages comprises 212 operational taxonomic units (OTUs). Sugar concentration showed the highest number of significant associations with OTUs of different phyla. The structure of the bacterial communities was different in both silage fermentation processes, showing that AZ silage has a shorter fermentation process than A silage. In addition, NGS demonstrated the effect of the type of maize and local conditions on silage fermentation and contributed to potential strategies to improve the quality of AZ silage.

scholarly journals The Wheat Microbiome Under Four Management Strategies, and Potential for Endophytes in Disease Protection

2017 ◽  
Vol 1 (3) ◽  
pp. 158-168 ◽  
Author(s):  
Kristi Gdanetz ◽  
Frances Trail
Keyword(s):  
Bacterial Communities ◽  
Management Strategy ◽  
Crop Yields ◽  
Management Strategies ◽  
Growing Season ◽  
Amplicon Sequencing ◽  
Antagonistic Activity ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Plant Organ

Manipulating plant-associated microbes to reduce disease or improve crop yields requires a thorough understanding of interactions within the phytobiome. Plants were sampled from a wheat/maize/soybean crop rotation site that implements four different crop management strategies. We analyzed the fungal and bacterial communities of leaves, stems, and roots of wheat throughout the growing season using 16S and fungal internal transcribed spacer 2 rRNA gene amplicon sequencing. The most prevalent operational taxonomic units (OTUs) were shared across all samples, although levels of the low-abundance OTUs varied. Endophytes were isolated from plants, and tested for antagonistic activity toward the wheat pathogen Fusarium graminearum. Antagonistic strains were assessed for plant protective activity in seedling assays. Our results suggest that microbial communities were strongly affected by plant organ and plant age, and may be influenced by management strategy.

scholarly journals Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hanna Sinkko ◽  
Iina Hepolehto ◽  
Christina Lyra ◽  
Johanna M. Rinta-Kanto ◽  
Anna Villnäs ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Environmental Problem ◽  
Oxygen Deficiency ◽  
Marine Ecosystems ◽  
Operational Taxonomic Units ◽  
Water Oxygen ◽  
Abundant Otus ◽  
Compositional Changes ◽  
Induced Changes ◽  
Sediment Bacterial Communities

Abstract Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.

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

2020 ◽  
Vol 113 (5) ◽  
pp. 707-717 ◽  
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

scholarly journals Mycobacteria in Minas cheese commercialized in open fairs in São Paulo, Brazil

2018 ◽  
Vol 55 (4) ◽  
pp. e146525
Author(s):  
Patricia Rossi Moriconi ◽  
Cássia Yumi Ikuta ◽  
Fábio Gregori ◽  
Gisele de Oliveira ◽  
Sheila de Oliveira ◽  
...  
Keyword(s):  
Cetylpyridinium Chloride ◽  
Raw Milk ◽  
Sao Paulo ◽  
Nucleotide Sequencing ◽  
Dairy Herds ◽  
Rrna Gene ◽  
São Paulo ◽  
Oral Transmission ◽  
Pcr Targeting ◽  
The City

Mycobacterium bovis is the causative agent of bovine tuberculosis, a disease that affects dairy herds throughout the Brazilian territory, constituting a neglected zoonosis transmitted by raw milk and its derivatives. In this study, we evaluated the presence of M. bovis and other mycobacteria in Minas cheese obtained from open fairs in the city of São Paulo between 2012 and 2013. Samples (n = 133) were decontaminated using hexa-cetylpyridinium chloride and seeded on Stonebrink–Leslie medium. The isolates were submitted to molecular identification by TB Multiplex PCR targeting the 16S rRNA gene and amplicon nucleotide sequencing. From 16 cheese samples (12%), we obtained 26 putative colonies of Mycobacterium spp., none of which belonged to any of the Mycobacterium tuberculosis, Mycobacterium avium, or Mycobacterium intracellulare complexes. Phylogenetic analysis showed that sample sequences were grouped in a clade that includes only non-tuberculous mycobacteria with proximity to sequences obtained from Mycobacterium novocastrense (3 sequences), Mycobacterium holsaticum (1 sequence), andMycobacterium elephantis (2 sequences). Although no epidemiological evidence was found regarding the importance of oral transmission of mycobacteria in healthy people, their importance in the immunosuppressed population remains uncertain.

scholarly journals Molecular characterisation of Cryptosporidium spp. in lambs in the South Central region of the State of São Paulo

2015 ◽  
Vol 67 (2) ◽  
pp. 441-446 ◽  
Author(s):  
A.S. Zucatto ◽  
M.C.C. Aquino ◽  
S.V. Inácio ◽  
R.N. Figueiredo ◽  
J.C. Pierucci ◽  
...  
Keyword(s):  
Central Region ◽  
18S Rrna Gene ◽  
Sao Paulo ◽  
The State ◽  
Rrna Gene ◽  
São Paulo ◽  
The South ◽  
Cryptosporidium Spp ◽  
South Central ◽  
One Year

Considering the proximity of sheep farmers to animals that are possibly diseased or releasing fecal oocysts into the environment and the marked pathogenicity in lambs, the aim of this study was to determine the occurrence and to molecularly characterize the infection by Cryptosporidium spp. in lambs in the South Central region of the state of São Paulo, Brazil. A total of 193 fecal samples were collected from sheep of several breeds, males and females, aged up to one year. Polymerase chain reaction (nested-PCR) was used to amplify DNA fragments from the subunit 18S rRNA gene and indicated 15% positivity; sequencing of amplified fragments was possible for 19 samples. Analysis of the obtained sequences showed that the identified species were Cryptosporidium xiaoi for 15 samples, constituting thus the first molecular characterization study of this Cryptosporidium species in Brazil. Cryptosporidium ubiquitum was identified for three samples and Cryptosporidium meleagridis for one sample; the latter two are considered zoonotic species.

scholarly journals Ancient DNA complements microfossil record in deep-sea subsurface sediments

2013 ◽  
Vol 9 (4) ◽  
pp. 20130283 ◽  
Author(s):  
Franck Lejzerowicz ◽  
Philippe Esling ◽  
Wojciech Majewski ◽  
Witold Szczuciński ◽  
Johan Decelle ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Deep Sea ◽  
Environmental Dna ◽  
Small Subunit ◽  
Marine Biodiversity ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Core Sediment ◽  
Subsurface Sediments ◽  
Sediment Layers

Deep-sea subsurface sediments are the most important archives of marine biodiversity. Until now, these archives were studied mainly using the microfossil record, disregarding large amounts of DNA accumulated on the deep-sea floor. Accessing ancient DNA (aDNA) molecules preserved down-core would offer unique insights into the history of marine biodiversity, including both fossilized and non-fossilized taxa. Here, we recover aDNA of eukaryotic origin across four cores collected at abyssal depths in the South Atlantic, in up to 32.5 thousand-year-old sediment layers. Our study focuses on Foraminifera and Radiolaria, two major groups of marine microfossils also comprising diverse non-fossilized taxa. We describe their assemblages in down-core sediment layers applying both micropalaeontological and environmental DNA sequencing approaches. Short fragments of the foraminiferal and radiolarian small subunit rRNA gene recovered from sedimentary DNA extracts provide evidence that eukaryotic aDNA is preserved in deep-sea sediments encompassing the last glacial maximum. Most aDNA were assigned to non-fossilized taxa that also dominate in molecular studies of modern environments. Our study reveals the potential of aDNA to better document the evolution of past marine ecosystems and opens new horizons for the development of deep-sea palaeogenomics.

scholarly journals Bottled aqua incognita: Microbiota assembly and dissolved organic matter diversity in natural mineral waters

2017 ◽  
Author(s):  
Celine C. Lesaulnier ◽  
Craig W. Herbold ◽  
Claus Pelikan ◽  
David Berry ◽  
Cédric Gérard ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Mineral Waters ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Natural Mineral ◽  
Operational Taxonomic Units ◽  
Abundant Otus ◽  
Low Concentrations ◽  
Carbon Molecules

ABSTRACTBackgroundNon-carbonated natural mineral waters contain microorganisms that regularly grow after bottling despite low concentrations of dissolved organic matter (DOM). Yet, the compositions of bottled water microbiota and organic substrates that fuel microbial activity, and how both change after bottling, are still largely unknown.ResultsWe performed a multifaceted analysis of microbiota and DOM diversity in twelve natural mineral waters from six European countries. 16S rRNA gene-based analyses showed that less than ten species-level operational taxonomic units (OTUs) dominated the bacterial communities in the water phase and associated with the bottle wall after a short phase of post-bottling growth. Members of the betaproteobacterial genera Curvibacter, Aquabacterium, and Polaromonas (Comamonadaceae) grew in most waters and represent ubiquitous, mesophilic, heterotrophic aerobes in bottled waters. Ultrahigh-resolution mass spectrometry of DOM in bottled waters and their corresponding source waters identified thousands of molecular formulae characteristic of mostly refractory, soil-derived DOM.ConclusionsThe bottle environment, including source water physicochemistry, selected for growth of a similar low-diversity microbiota across various bottled waters. Relative abundance changes of hundreds of multi-carbon molecules were related to growth of less than ten abundant OTUs. We thus speculate that individual bacteria cope with oligotrophic conditions by simultaneously consuming diverse DOM molecules.

scholarly journals Microbial communities associated with sediments and polymetallic nodules of the Peru Basin

2020 ◽  
Author(s):  
Massimiliano Molari ◽  
Felix Janssen ◽  
Tobias Vonnahme ◽  
Frank Wenzhöfer ◽  
Antje Boetius
Keyword(s):  
Community Composition ◽  
Deep Sea ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Polymetallic Nodules ◽  
Relevant Role ◽  
Bacterial And Archaeal Communities ◽  
Clarion Clipperton Fracture Zone ◽  
And Function

Abstract. Industrial-scale mining of deep-sea polymetallic nodules will need to remove nodules in large areas of the seafloor. The regrowth of the nodules by metal precipitation is estimated to take millions of years. Thus for future mining impact studies, it is crucial to understand the role of nodules in shaping microbial diversity and function in deep-sea environments. Here we investigated microbial community composition based on 16S rRNA gene sequences retrieved from sediments and nodules of the Peru Basin (> 4100 m water depth). The nodule field of the Peru Basin showed a typical deep-sea microbiome, with dominance of the classes Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, and Acidimicrobiia. Nodules and sediments host distinct bacterial and archaeal communities, with nodules showing lower diversity and a higher proportion of sequences related to potential metal-cycling bacteria (i.e. Magnetospiraceae, Hyphomicrobiaceae), bacterial and archaeal nitrifiers (i.e. AqS1, unclassified Nitrosomonadaceae, Nitrosopumilus, Nitrospina, Nitrospira), and bacterial sequences found in ocean crust, nodules, hydrothermal deposits and sessile fauna. Sediment and nodule communities overall shared a low proportion of Operational Taxonomic Units (OTU; 21 % for Bacteria and 19 % for Archaea). Our results show that nodules represent a specific ecological niche (i.e. hard substrate, high metal concentrations and sessile fauna), with a potentially relevant role in organic carbon degradation. Differences in nodule community composition (e.g. Mn-cycling bacteria, nitrifiers) between the Clarion-Clipperton Fracture Zone (CCZ) and the Peru Basin suggest that changes in environmental setting (i.e. sedimentation rates) play also a significant role in structuring the nodule microbiome.

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