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

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.

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

Microbiology Resource Announcements ◽

10.1128/mra.00761-20 ◽

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%).

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Differentiation of Phylogenetically Related Slowly Growing Mycobacteria Based on 16S-23S rRNA Gene Internal Transcribed Spacer Sequences

Journal of Clinical Microbiology ◽

10.1128/jcm.36.1.139-147.1998 ◽

1998 ◽

Vol 36 (1) ◽

pp. 139-147 ◽

Cited By ~ 190

Author(s):

Andreas Roth ◽

Marga Fischer ◽

Mohamed E. Hamid ◽

Sabine Michalke ◽

Wolfgang Ludwig ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

16S Rdna ◽

Internal Transcribed Spacer ◽

Sequence Divergence ◽

Comparative Sequence Analysis ◽

Its Sequences ◽

23S Rrna ◽

Rrna Gene ◽

Its Sequencing

Interspecific polymorphisms of the 16S rRNA gene (rDNA) are widely used for species identification of mycobacteria. 16S rDNA sequences, however, do not vary greatly within a species, and they are either indistinguishable in some species, for example, in Mycobacterium kansasii and M. gastri, or highly similar, for example, in M. malmoense and M. szulgai. We determined 16S-23S rDNA internal transcribed spacer (ITS) sequences of 60 strains in the genus Mycobacterium representing 13 species (M. avium, M. conspicuum, M. gastri, M. genavense, M. kansasii,M. malmoense, M. marinum, M. shimoidei, M. simiae, M. szulgai,M. triplex, M. ulcerans, and M. xenopi). An alignment of these sequences together with additional sequences available in the EMBL database (for M. intracellulare, M. phlei, M. smegmatis, and M. tuberculosis) was established according to primary- and secondary-structure similarities. Comparative sequence analysis applying different treeing methods grouped the strains into species-specific clusters with low sequence divergence between strains belonging to the same species (0 to 2%). The ITS-based tree topology only partially correlated to that based on 16S rDNA, but the main branching orders were preserved, notably, the division of fast-growing from slowly growing mycobacteria, separate branching for M. simiae, M. genavense, and M. triplex, and distinct branches for M. xenopi and M. shimoidei. Comparisons of M. gastri with M. kansasii and M. malmoense with M. szulgairevealed ITS sequence similarities of 93 and 88%, respectively.M. marinum and M. ulcerans possessed identical ITS sequences. Our results show that ITS sequencing represents a supplement to 16S rRNA gene sequences for the differentiation of closely related species. Slowly growing mycobacteria show a high sequence variation in the ITS; this variation has the potential to be used for the development of probes as a rapid approach to mycobacterial identification.

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

Applied and Environmental Microbiology ◽

10.1128/aem.02173-17 ◽

2018 ◽

Vol 84 (9) ◽

Cited By ~ 15

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.

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Microbacterium oryzae sp. nov., an actinobacterium isolated from rice field soil

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.046870-0 ◽

2013 ◽

Vol 63 (Pt_7) ◽

pp. 2442-2449 ◽

Cited By ~ 14

Author(s):

Prabla Kumari ◽

Saumya Bandyopadhyay ◽

Subrata K. Das

Keyword(s):

16S Rrna ◽

Type Species ◽

Gene Sequence ◽

Rice Field ◽

Rrna Gene ◽

Field Soil ◽

Rrna Gene Sequence ◽

Content Type ◽

Link Type ◽

Rice Field Soil

A novel aerobic soil actinobacterium (strain MB10T) belonging to the genus Microbacterium was isolated from rice field soil samples collected from Jagatpur, Orissa, India. Cells were Gram-stain positive, short rod-shaped and motile. The strain was oxidase-negative and catalase-positive. Heterotrophic growth was observed at pH 5.0–11.0 and at 16–37 °C; optimum growth was observed at 28 °C and pH 7.0–9.0. The DNA G+C content was 71.6 mol%. Predominant cellular fatty acids of strain MB10T were iso-C14 : 0, anteiso-C15 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0. Cell wall sugars were galactose, glucose and rhamnose. The major isoprenoid quinones were MK-9 (10 %), MK-10 (43 %) and MK-11 (36 %). The peptidoglycan represents the peptidoglycan type B2β. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid and unknown glycolipids. 16S rRNA gene sequence identity revealed the strain MB10T clustered within the radiation of the genus Microbacterium and showed 99.2 % similarity with Microbacterium barkeri DSM 20145T. However, DNA–DNA similarity study was 37.0 % with Microbacterium barkeri DSM 20145T, the nearest phylogenetic relative. On the basis of phenotypic and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA–DNA reassociation studies, it is proposed that strain MB10T represents a novel species of the genus Microbacterium , for which the name Microbacterium oryzae sp. nov. is proposed; the type strain is MB10T ( = JCM 16837T = DSM 23396 T ).

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The evolution of realized niches within freshwater Synechococcus

10.1101/678375 ◽

2019 ◽

Author(s):

Nicolas Tromas ◽

Zofia E. Taranu ◽

Mathieu Castelli ◽

Juliana S. M. Pimentel ◽

Daniel A. Pereira ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Environmental Parameters ◽

Amplicon Sequencing ◽

Fundamental Question ◽

Rrna Gene ◽

Biological Interactions ◽

Sequencing Data ◽

Evolutionary Time ◽

Genus Level

SummaryUnderstanding how ecological traits have changed over evolutionary time is a fundamental question in biology. Specifically, the extent to which more closely-related organisms share similar ecological preferences due to phylogenetic conservation – or if they are forced apart by competition – is still debated. Here we explored the co-occurrence patterns of freshwater cyanobacteria at the sub-genus level to investigate whether more closely-related taxa share more similar niches, and to what extent these niches were defined by abiotic or biotic variables. We used deep 16S rRNA gene amplicon sequencing and measured several abiotic environmental parameters (nutrients, temperature, etc.) in water samples collected over time and space in Furnas Reservoir, Brazil. We found that relatively more closely-related Synechococcus (in the continuous range of 93-100% nucleotide identity in 16S) had an increased tendency to co-occur with one another (i.e. had similar realized niches). This tendency could not be easily explained by shared preferences for measured abiotic niche dimensions. Thus, commonly measured abiotic parameters might not be sufficient to characterize, nor to predict community assembly or dynamics. Rather, co-occurrence between Synechococcus and the surrounding community (whether or not they represent true biological interactions) may be a more sensitive measure of realized niches. Overall, our results suggest that realized niches are phylogenetically conserved, at least at the sub-genus level and at the resolution of the 16S marker. Determining how these results generalize to other genera and at finer genetic resolution merits further investigation.Originality-Significance StatementWe address a fundamental question in ecology and evolution: how do niche preferences change over evolutionary time? Using time-series analysis of 16S rRNA gene amplicon sequencing data, we develop an approach to highlight the importance of biotic factors in defining realized niches, and show how niche preferences change proportionally with the 16S gene molecular clock within the genus Synechococcus. Ours is also one of few studies on the ecology of freshwater Synechococcus, adding significantly to our knowledge about this abundant and widespread lineage of Cyanobacteria.

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

Microbiology Resource Announcements ◽

10.1128/mra.00374-21 ◽

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 .

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The archives are half-empty: a field-wide assessment of the availability of microbial community sequencing data

10.1101/2020.04.28.063271 ◽

2020 ◽

Author(s):

Stephanie D. Jurburg ◽

Maximilian Konzack ◽

Nico Eisenhauer ◽

Anna Heintz-Buschart

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Amplicon Sequencing ◽

Data Reuse ◽

Rrna Gene ◽

Data Loss ◽

Sequencing Data ◽

Data Archiving ◽

The 16S Rrna Gene ◽

Over Time

AbstractThe sequencing revolution has resulted in the explosive growth of public genetic repositories. These repositories now hold invaluable collections of 16S rRNA gene amplicon sequences, but the extent to which the currently archived data is findable, accessible, and reusable has not been evaluated. We conducted a field-wide assessment of the availability and state of publicly archived 16S rRNA gene amplicon sequencing data. Using custom-built pattern-based text extraction algorithms, we searched 26,927 publications in 17 microbiology or microbial ecology journals, and identified 2,015 studies which performed 16S rRNA gene amplicon sequencing. We found, for example, that 7.2% of these had not been made public at the time of analysis, a trend which increased over time. Of the 635 studies targeting the V3-V4 region of the 16S rRNA gene, 40.3% contained data which was not available or not reusable, and for 25.5% of the studies, faults in data formatting or data labelling were likely to create obstacles in data reuse. Taken together, only 34% of these datasets had potentially reusable data. Our study reveals significant gaps in the availability of currently deposited community sequencing data, identifies major contributors to data loss, and offers suggestions for improving data archiving practices in the future.

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

Microbiology Resource Announcements ◽

10.1128/mra.00851-19 ◽

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.

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Molecular Detection of Campylobacter spp. in California Gull (Larus californicus) Excreta

Applied and Environmental Microbiology ◽

10.1128/aem.00018-11 ◽

2011 ◽

Vol 77 (14) ◽

pp. 5034-5039 ◽

Cited By ~ 25

Author(s):

Jingrang Lu ◽

Hodon Ryu ◽

Jorge W. Santo Domingo ◽

John F. Griffith ◽

Nicholas Ashbolt

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Molecular Detection ◽

Rrna Gene ◽

Fecal Indicators ◽

Sequencing Data ◽

Content Type ◽

Human Illness ◽

Campylobacter Spp

ABSTRACTWe examined the prevalence, quantity, and diversity ofCampylobacterspecies in the excreta of 159 California gull (Larus californicus) samples using culture-, PCR-, and quantitative PCR (qPCR)-based detection assays.Campylobacterprevalence and abundance were relatively high in the gull excreta examined; however,C. jejuniandC. lariwere detected in fewer than 2% of the isolates and DNA extracts from the fecal samples that tested positive. Moreover, molecular and sequencing data indicated that mostL. californicuscampylobacters were novel (<97% 16S rRNA gene sequence identity to knownCampylobacterspecies) and not closely related to species commonly associated with human illness.Campylobacterestimates were positively related with those of fecal indicators, including a gull fecal marker based on theCatellicoccus marimammalium16S rRNA gene.

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16S rRNA Gene Amplicon Sequencing Data of the Iron Quadrangle Ferruginous Caves (Brazil) Shows the Importance of Conserving This Singular and Threatened Geosystem

Diversity ◽

10.3390/d13100494 ◽

2021 ◽

Vol 13 (10) ◽

pp. 494

Author(s):

Camila G. C. Lemes ◽

Morghana M. Villa ◽

Érica B. Felestrino ◽

Luiza O. Perucci ◽

Renata A. B. Assis ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Diversity ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sequencing Data ◽

Metabolic Potential ◽

Microbial Life ◽

Iron Quadrangle ◽

Abundance And Diversity

The Iron Quadrangle (IQ) is one of the main iron ore producing regions of the world. The exploitation of its reserves jeopardizes the high biological endemism associated with this region. This work aimed to understand the diversity and bacterial potential associated with IQ caves. Floor and ceiling samples of seven ferruginous caves and one quartzite cave were collected, and their microbial relative abundance and diversity were established by 16S rRNA gene amplicon sequencing data. The results showed that ferruginous caves present higher microbial abundance and greater microbial diversity compared to the quartzite cave. Many species belonging to genera found in these caves, such as Pseudonocardia and Streptacidiphilus, are known to produce biomolecules of biotechnological interest as macrolides and polyketides. Moreover, comparative analysis of microbial diversity and metabolic potential in a biofilm in pendant microfeature revealed that the microbiota associated with this structure is more similar to the floor rather than ceiling samples, with the presence of genera that may participate in the genesis of these cavities, for instance, Ferrovum, Geobacter, and Sideroxydans. These results provide the first glimpse of the microbial life in these environments and emphasize the need of conservation programs for these areas, which are under intense anthropogenic exploration.

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