Rare unclassified 16S rRNA operational taxonomic units from the uncharted Engaño Bay (Argentinean Patagonia)

2018 ◽  
Vol 64 (1) ◽  
pp. 91-96
Author(s):  
Andrea Y. Calvo ◽  
Julieta M. Manrique ◽  
Leandro R. Jones
Keyword(s):  
16S Rrna ◽  
Community Dynamics ◽  
Sequence Data ◽  
River Estuary ◽  
Fragmented Habitats ◽  
Operational Taxonomic Units ◽  
Microbial Community Dynamics ◽  
Argentinean Patagonia ◽  
Culture Independent ◽  
Taxonomic Assignments

Rare microbes make up most of the diversity of marine microbiomes, and recent works have highlighted their importance for microbial community dynamics and in fragmented habitats. Rare taxa have been infrequently studied in comparison with abundant groups, and rare unclassified sequences are common in culture-independent studies. Here, we describe a detailed analysis of nonclassifiable sequences from the Chubut river estuary at the Argentinean Patagonia. Standard taxonomic assignments of environmental 16S rRNA sequences resulted in about 13% unclassified operational taxonomic units (OTUs). The potential affiliations of these OTUs could be narrowed by mapping the classification software assignments on a phylogeny obtained directly from our environmental sequence data. Customized BLAST analyses were remarkably consistent with these phylogenetic assignments, especially when the unclassified OTUs were blasted against sequences from cultured and type microorganisms. In addition, our BLAST analyses revealed significant similarities between several unclassified OTUs and a plethora of unclassified sequences from around the world. Further phylogenetic comparisons with 6194 carefully selected reference sequences showed that these unclassified sequences may correspond to 5 unnamed groups, possibly encompassing ranks from subclass to family inside the Alphaproteobacteria, and to an unknown Gracilibacteria lineage. Overall, these results demonstrate the value of straight phylogenetic analysis, customized BLAST searches, and comparisons with sequences from type material, for the systematic study of rare unclassified sequences.

scholarly journals Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

2009 ◽  
Vol 75 (23) ◽  
pp. 7537-7541 ◽  
Author(s):  
Patrick D. Schloss ◽  
Sarah L. Westcott ◽  
Thomas Ryabin ◽  
Justine R. Hall ◽  
Martin Hartmann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Software Package ◽  
Sequence Data ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Laptop Computer ◽  
Operational Taxonomic Units ◽  
Β Diversity ◽  
Single Piece

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

scholarly journals Phylogenetic and Chemical Diversity of a Hybrid-Isoprenoid-Producing Streptomycete Lineage

2013 ◽  
Vol 79 (22) ◽  
pp. 6894-6902 ◽  
Author(s):  
Kelley A. Gallagher ◽  
Kristin Rauscher ◽  
Laura Pavan Ioca ◽  
Paul R. Jensen
Keyword(s):  
Secondary Metabolites ◽  
Secondary Metabolite ◽  
Sequence Data ◽  
Environmental Dna ◽  
Chemical Diversity ◽  
Phenotypic Trait ◽  
Content Type ◽  
Operational Taxonomic Units ◽  
Culture Independent ◽  
Structural Classes

ABSTRACTStreptomycesspecies dedicate a large portion of their genomes to secondary metabolite biosynthesis. A diverse and largely marine-derived lineage within this genus has been designated MAR4 and identified as a prolific source of hybrid isoprenoid (HI) secondary metabolites. These terpenoid-containing compounds are common in nature but rarely observed as bacterial secondary metabolites. To assess the phylogenetic diversity of the MAR4 lineage, complementary culture-based and culture-independent techniques were applied to marine sediment samples collected off the Channel Islands, CA. The results, including those from an analysis of publically available sequence data and strains isolated as part of prior studies, placed 40 new strains in the MAR4 clade, of which 32 originated from marine sources. When combined with sequences cloned from environmental DNA, 28 MAR4 operational taxonomic units (0.01% genetic distance) were identified. Of these, 82% consisted exclusively of either cloned sequences or cultured strains, supporting the complementarity of these two approaches. Chemical analyses of diverse MAR4 strains revealed the production of five different HI structure classes. All 21 MAR4 strains tested produced at least one HI class, with most strains producing from two to four classes. The two major clades within the MAR4 lineage displayed distinct patterns in the structural classes and the number and amount of HIs produced, suggesting a relationship between taxonomy and secondary metabolite production. The production of HI secondary metabolites appears to be a phenotypic trait of the MAR4 lineage, which represents an emerging model with which to study the ecology and evolution of HI biosynthesis.

scholarly journals Ibuprofen Degradation and Associated Bacterial Communities in Hyporheic Zone Sediments

2020 ◽  
Vol 8 (8) ◽  
pp. 1245
Author(s):  
Cyrus Rutere ◽  
Kirsten Knoop ◽  
Malte Posselt ◽  
Adrian Ho ◽  
Marcus A. Horn
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Hyporheic Zone ◽  
Community Dynamics ◽  
Environmental Concern ◽  
Transformation Products ◽  
Pollutant Removal ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Microbial Community Dynamics

Ibuprofen, a non-steroidal anti-inflammatory pain reliever, is among pharmaceutical residues of environmental concern ubiquitously detected in wastewater effluents and receiving rivers. Thus, ibuprofen removal potentials and associated bacteria in the hyporheic zone sediments of an impacted river were investigated. Microbially mediated ibuprofen degradation was determined in oxic sediment microcosms amended with ibuprofen (5, 40, 200, and 400 µM), or ibuprofen and acetate, relative to an un-amended control. Ibuprofen was removed by the original sediment microbial community as well as in ibuprofen-enrichments obtained by re-feeding of ibuprofen. Here, 1-, 2-, 3-hydroxy- and carboxy-ibuprofen were the primary transformation products. Quantitative real-time PCR analysis revealed a significantly higher 16S rRNA abundance in ibuprofen-amended relative to un-amended incubations. Time-resolved microbial community dynamics evaluated by 16S rRNA gene and 16S rRNA analyses revealed many new ibuprofen responsive taxa of the Acidobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Latescibacteria, and Proteobacteria. Two ibuprofen-degrading strains belonging to the genera Novosphingobium and Pseudomonas were isolated from the ibuprofen-enriched sediments, consuming 400 and 300 µM ibuprofen within three and eight days, respectively. The collective results indicated that the hyporheic zone sediments sustain an efficient biotic (micro-)pollutant degradation potential, and hitherto unknown microbial diversity associated with such (micro)pollutant removal.

scholarly journals Metagenomics: Retrospect and Prospects in High Throughput Age

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Satish Kumar ◽  
Kishore Kumar Krishnani ◽  
Bharat Bhushan ◽  
Manoj Pandit Brahmane
Keyword(s):  
Community Dynamics ◽  
Full Potential ◽  
Basic Study ◽  
Independent Manner ◽  
Microbial Community Dynamics ◽  
Current State ◽  
Culture Independent ◽  
Almost All ◽  
Insight Into ◽  
Generation Sequencing

In recent years, metagenomics has emerged as a powerful tool for mining of hidden microbial treasure in a culture independent manner. In the last two decades, metagenomics has been applied extensively to exploit concealed potential of microbial communities from almost all sorts of habitats. A brief historic progress made over the period is discussed in terms of origin of metagenomics to its current state and also the discovery of novel biological functions of commercial importance from metagenomes of diverse habitats. The present review also highlights the paradigm shift of metagenomics from basic study of community composition to insight into the microbial community dynamics for harnessing the full potential of uncultured microbes with more emphasis on the implication of breakthrough developments, namely, Next Generation Sequencing, advanced bioinformatics tools, and systems biology.

scholarly journals Phylogenetic Comparisons of Bacterial Communities from Serpentine and Nonserpentine Soils

2006 ◽  
Vol 72 (11) ◽  
pp. 6965-6971 ◽  
Author(s):  
David K. Oline
Keyword(s):  
16S Rrna ◽  
Bacterial Communities ◽  
Regional Scale ◽  
Serpentine Soils ◽  
Operational Taxonomic Units ◽  
Microbial Biogeography ◽  
Soil Bacterial Communities ◽  
Culture Independent ◽  
Control Community ◽  
16S Rrna Clone Libraries

ABSTRACT I present the results of a culture-independent survey of soil bacterial communities from serpentine soils and adjacent nonserpentine comparator soils using a variety of newly developed phylogenetically based statistical tools. The study design included site-based replication of the serpentine-to-nonserpentine community comparison over a regional scale (∼100 km) in Northern California and Southern Oregon by producing 16S rRNA clone libraries from pairs of samples taken on either side of the serepentine-nonserpentine edaphic boundary at three geographical sites. At the division level, the serpentine and nonserpentine communities were similar to each other and to previous data from forest soils. Comparisons of both richness and Shannon diversity produced no significant differences between any of the libraries, but the vast majority of phylogenetically based tests were significant, even with only 50 sequences per library. These results suggest that most samples were distinct, consisting of a collection of lineages generally not found in other samples. The pattern of results showed that serpentine communities tended to be more similar to each other than they were to nonserpentine communities, and these differences were at a lower taxonomic scale. Comparisons of two nonserpentine communities generally showed differences, and some results suggest that the geographical site may control community composition as well. These results show the power of phylogenetic tests to discern differences between 16S rRNA libraries compared to tests that discard DNA data to bin sequences into operational taxonomic units, and they stress the importance of replication at larger scales for inferences regarding microbial biogeography.

scholarly journals OptiClust: Improved method for assigning amplicon-based sequence data to operational taxonomic units

2016 ◽  
Author(s):  
Sarah L. Westcott ◽  
Patrick D. Schloss
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Significant Advance ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Operational Taxonomic Units ◽  
Computational Bottleneck

AbstractAssignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. Although this has been an active area of research, it has been difficult to overcome the time and memory demands while improving the quality of the OTU assignments. Here we developed a new OTU assignment algorithm that iteratively reassigns sequences to new OTUs to optimize the Matthews correlation coefficient (MCC), a measure of the quality of OTU assignments. To assess the new algorithm, OptiClust, we compared it to ten other algorithms using 16S rRNA gene sequences from two simulated and four natural communities. Using the OptiClust algorithm, the MCC values averaged 15.2 and 16.5% higher than the OTUs generated when we used the average neighbor and distance-based greedy clustering with VSEARCH, respectively. Furthermore, on average, OptiClust was 94.6-times faster than the average neighbor algorithm and just as fast as distance-based greedy clustering with VSEARCH. An empirical analysis of the efficiency of the algorithms showed that the time and memory required to perform the algorithm scaled quadratically with the number of unique sequences in the dataset. The significant improvement in the quality of the OTU assignments over previously existing methods will significantly enhance downstream analysis by limiting the splitting of similar sequences into separate OTUs and merging of dissimilar sequences into the same OTU. The development of the OptiClust algorithm represents a significant advance that is likely to have numerous other applications.

scholarly journals Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

PLoS ONE ◽  
2014 ◽  
Vol 9 (4) ◽  
pp. e93827 ◽  
Author(s):  
Rachel Poretsky ◽  
Luis M. Rodriguez-R ◽  
Chengwei Luo ◽  
Despina Tsementzi ◽  
Konstantinos T. Konstantinidis
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Dynamics ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Microbial Community Dynamics
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