Microspatial gene expression patterns in the Amazon River Plume

Satinsky, Brandon M.; Crump, Byron C.; Smith, Christa B.; Sharma, Shalabh; Zielinski, Brian L.; Doherty, Mary K.; Meng, Jun; Sun, Sheng; Medeiros, Patricia M.; Paul, John H.; Coles, Victoria J.; Yager, Patricia L.; Moran, Mary Ann

doi:10.1073/pnas.1402782111

Cited by 135 publications

(132 citation statements)

References 26 publications

(32 reference statements)

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“…Similar patterns were observed for ratios based on 16S rRNA gene amplicons and transcripts from metatranscriptomes (rRNA:rDNA; Supplementary Figure S4). Although RNA:DNA ratios, based either on target genes or community gene pools, have been used as proxies for metabolic activity (Campbell and Yu, 2011;Hunt et al, 2013;Satinsky et al, 2014), linking ratios to activity is tenuous. Notably, as RNA/DNA ratios are based on proportional abundances, increases in taxon representation in the transcriptome can reflect either increases in the activity of the target taxon or decreases in the activity of other organisms.…”

Section: Rna:dna Ratiosmentioning

confidence: 99%

“…Such studies risk excluding important information about contributions from PA cells, larger non-PA cells or metabolic substrates in PA fractions. Furthermore, only a single study (Satinsky et al, 2014) has examined community gene expression (metatranscriptomes) in PA versus FL communities. When coupled to measurements of metabolic rates, size-fractionated metatranscriptomics can help identify the drivers, magnitudes and spatial scales of biogeochemistry in the oceans.…”

Section: Introductionmentioning

confidence: 99%

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Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

et al. 2015

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The genetic composition of marine microbial communities varies at the microscale between particleassociated (PA; 41.6 μm) and free-living (FL; 0.2-1.6 μm) niches. It remains unclear, however, how metabolic activities differ between PA and FL fractions. We combined rate measurements with metatranscriptomics to quantify PA and FL microbial activity in the oxygen minimum zone (OMZ) of the Eastern Tropical North Pacific, focusing on dissimilatory processes of the nitrogen (N) cycle. Bacterial gene counts were 8-to 15-fold higher in the FL compared with the PA fraction. However, rates of all measured N cycle processes, excluding ammonia oxidation, declined significantly following particle (41.6 μm) removal. Without particles, rates of nitrate reduction to nitrite (1.5-9.4 nM N d − 1 ) fell to zero and N 2 production by denitrification (0.5-1.7 nM N d − 1 ) and anammox (0.3-1.9 nM N d − 1 ) declined by 53-85%. The proportional representation of major microbial taxa and N cycle gene transcripts in metatranscriptomes followed fraction-specific trends. Transcripts encoding nitrate reductase were uniform among PA and FL fractions, whereas anammox-associated transcripts were proportionately enriched up to 15-fold in the FL fraction. In contrast, transcripts encoding enzymes for N 2 O and N 2 production by denitrification were enriched up to 28-fold in PA samples. These patterns suggest that the majority of N cycle activity, excluding N 2 O and N 2 production by denitrification, is confined to a FL majority that is critically dependent on access to particles, likely as a source of organic carbon and inorganic N. Variable particle distributions may drive heterogeneity in N cycle activity and gene expression in OMZs.

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Section: Rna:dna Ratiosmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

et al. 2015

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“…For Sterivex filters, the filter was removed from the casing by cracking the housing with pliers, sliced on a sterile cutting board and added to the DNA extraction buffer with the original membrane filter. An internal genomic DNA standard (Thermus thermophilus HB8 genomic DNA) was also added as a means to normalize sequencing coverage across samples (Satinsky et al, 2014). The standard genomic DNA was spiked into each individual sample in a known abundance (8.4 ng l À 1 filtered) before the initiation of cell lysis.…”

Section: Sample Collectionmentioning

confidence: 99%

“…In brief, after the filters were broken, as described above for DNA sample filters, they were transferred to a lysis solution consisting of 8 ml of RLT Lysis Solution (Qiagen, Valencia, CA, USA) and 3 g of RNA PowerSoil beads (Mo-Bio, Carlsbad, CA, USA). Two synthesized mRNA standards, which were 916 and 970 nt in length, were synthesized from the commercial vectors pTXB1 vector (New England Biolabs, Ipswich, MA, USA) and pFN18A Halotag T7 Flexi Vector (Promega, Madison, WI, USA) respectively, and were added individually to the prepared lysis tubes in known copy numbers (pTXB1 ¼ 2.104 Â 10 10 copies; pFN18A ¼ 1.172 Â 10 10 copies) before initiation of cell lysis (Satinsky et al, 2014). Tubes containing the filter pieces and lysis solution were vortexed for 10 min, and RNA was purified from cell lysate using the RNeasy Kit (Qiagen).…”

Section: Sample Collectionmentioning

confidence: 99%

Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume

et al. 2014

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Biological N 2 fixation is an important nitrogen source for surface ocean microbial communities. However, nearly all information on the diversity and gene expression of organisms responsible for oceanic N 2 fixation in the environment has come from targeted approaches that assay only a small number of genes and organisms. Using genomes of diazotrophic cyanobacteria to extract reads from extensive meta-genomic and -transcriptomic libraries, we examined diazotroph diversity and gene expression from the Amazon River plume, an area characterized by salinity and nutrient gradients. Diazotroph genome and transcript sequences were most abundant in the transitional waters compared with lower salinity or oceanic water masses. We were able to distinguish two genetically divergent phylotypes within the Hemiaulus-associated Richelia sequences, which were the most abundant diazotroph sequences in the data set. Photosystem (PS)-II transcripts in Richelia populations were much less abundant than those in Trichodesmium, and transcripts from several Richelia PS-II genes were absent, indicating a prominent role for cyclic electron transport in Richelia. In addition, there were several abundant regulatory transcripts, including one that targets a gene involved in PS-I cyclic electron transport in Richelia. High sequence coverage of the Richelia transcripts, as well as those from Trichodesmium populations, allowed us to identify expressed regions of the genomes that had been overlooked by genome annotations. High-coverage genomic and transcription analysis enabled the characterization of distinct phylotypes within diazotrophic populations, revealed a distinction in a core process between dominant populations and provided evidence for a prominent role for noncoding RNAs in microbial communities.

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“…Independientemente de la influencia oceánica, estas comunidades muestran cambios en su estructura atribuidos a las partículas en suspensión provenientes de ríos, escurrimientos o surgencias (Boeuf et al 2013, Ameryk et al 2014, Satinsky et al 2014, Aylward et al 2015, Mueller et al 2015. En estos ambientes, es posible diferenciar una comunidad adherida a materia orgánica y otra de vida libre (Smith et al 2013, Bižić-Ionescu et al 2014, Mohit et al 2014, Simon et al 2014).…”

Section: S Rrnaunclassified

The 16S rRNA gene in the study of marine microbial communities

et al. 2015

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ABSTRACT. New sequencing technologies and analytical capabilities have stimulated the study of microbial communities from specific environments, enabling researchers to understand the complexity of those systems. The 16S rRNA gene has proved very useful in describing the diversity and characterization of marine microbial communities, particularly of uncultivated organisms. The development of new sequencing techniques has contributed to the exponential increase in the number of reported 16S rRNA sequences as barcodes for microorganisms, forcing a review of concepts and methods for the taxonomic classification of these organisms. Manipulation and analysis of large amounts of genetic information have prompted the development of specific databases, specialized algorithms, and computational tools to compare thousands of such sequences and make a taxonomic assignment. Complete 16S rRNA sequences are thus needed for accurate and reproducible taxonomy assignment in the study of marine bacterial communities.Key words: metagenomics, marine microbial communities, 16S rRNA databases. RESUMEN. Las nuevas tecnologías de secuenciación y capacidades analíticas han estimulado el estudio de las comunidades microbianas deambientes específicos, lo cual ha permitido conocer la complejidad de estos sistemas. El gen ARNr 16S ha demostrado ser de gran utilidad para describir y caracterizar las comunidades microbianas marinas, especialmente los organismos no cultivados. Las nuevas técnicas de secuenciación han contribuido al incremento exponencial de registro de secuencias, aunque parciales, del ARNr 16S como elemento de código de barras para microorganismos. Consecuentemente, ha sido necesaria una revisión de conceptos y métodos de clasificación taxonómica para estos organismos. El manejo y análisis de una gran cantidad de información génica han impulsado el desarrollo de bases de datos específicas, algoritmos y herramientas computacionales especializadas para comparar miles de secuencias semejantes y hacer la asignación taxonómica. Por lo tanto, las secuencias completas del ARNr 16S son necesarias para una asignación taxonómica certera y reproducible en los estudios de comunidades microbianas marinas.Palabras clave: metagenómica, comunidades microbianas marinas, bases de datos ARNr 16S.

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Microspatial gene expression patterns in the Amazon River Plume

Cited by 135 publications

References 26 publications

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume

The 16S rRNA gene in the study of marine microbial communities

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