Quantitative Microbial Ecology through Stable Isotope Probing

Hungate, Bruce A.; Mau, Rebecca L.; Schwartz, Egbert; Caporaso, J. Gregory; Dijkstra, Paul; Gestel, Natasja van; Koch, Benjamin J.; Liu, Cindy M.; McHugh, Theresa A.; Marks, Jane C.; Morrissey, Ember M.; Price, Lance B.

doi:10.1128/aem.02280-15

Cited by 258 publications

(342 citation statements)

References 66 publications

Supporting

Mentioning

334

Contrasting

Unclassified

Order By: Relevance

“…We defined DNA-SIP incorporation similar to Nelson and Carlson (2012) and Hungate et al (2015) on the basis of a comparison of the relative distribution of an OTU across the CsCl density gradient in a control ( 12 C and 14 N substrate added) versus an experimental ( 13 C and 15 N substrate added) incubation. OTUs incorporating the label were defined as those OTUs that exhibited a relatively unimodal distribution in the CsCl gradient and whose peak buoyant density (BD) was shifted 40.012 g ml − 1 between the experiment and the control (similar to Buckley et al, 2007a).…”

Section: Bioinformatic Analysismentioning

confidence: 99%

“…To this end, we performed DNA stable-isotope probing (SIP) using isotopically labeled ( 13 C and 15 N) proteins from the picoeukaryotic phytoplankter Micromonas pusilla. We coupled SIP with high-throughput Illumina sequencing of 16S small subunit ribosomal RNA (rRNA) genes (Hungate et al, 2015;Morando and Capone, in review) in three different size fractions to identify protein assimilation by individual bacterial and archaeal operational taxonomic units (OTUs). We performed the incubations at a station within the coastal transition zone of the Central California Current, where there is a rich contextual background on biogeochemistry (for example, Collins et al, 2003), and where M. pusilla is a resident of the phytoplankton community (Thomsen and Buck, 1998).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

et al. 2016

View full text Add to dashboard Cite

Dissolved organic nitrogen (DON) supports a significant amount of heterotrophic production in the ocean. Yet, to date, the identity and diversity of microbial groups that transform DON are not well understood. To better understand the organisms responsible for transforming high molecular weight (HMW)-DON in the upper ocean, isotopically labeled protein extract from Micromonas pusilla, a eukaryotic member of the resident phytoplankton community, was added as substrate to euphotic zone water from the central California Current system. Carbon and nitrogen remineralization rates from the added proteins ranged from 0.002 to 0.35 μmol C l − 1 per day and 0.03 to 0.27 nmol N l − 1 per day. DNA stable-isotope probing (DNA-SIP) coupled with high-throughput sequencing of 16S rRNA genes linked the activity of 77 uncultivated freeliving and particle-associated bacterial and archaeal taxa to the utilization of Micromonas protein extract. The high-throughput DNA-SIP method was sensitive in detecting isotopic assimilation by individual operational taxonomic units (OTUs), as substrate assimilation was observed after only 24 h. Many uncultivated free-living microbial taxa are newly implicated in the cycling of dissolved proteins affiliated with the Verrucomicrobia, Planctomycetes, Actinobacteria and Marine Group II (MGII) Euryarchaeota. In addition, a particle-associated community actively cycling DON was discovered, dominated by uncultivated organisms affiliated with MGII, Flavobacteria, Planctomycetes, Verrucomicrobia and Bdellovibrionaceae. The number of taxa assimilating protein correlated with genomic representation of TonB-dependent receptor (TBDR)-encoding genes, suggesting a possible role of TBDR in utilization of dissolved proteins by marine microbes. Our results significantly expand the known microbial diversity mediating the cycling of dissolved proteins in the ocean.

show abstract

Section: Bioinformatic Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

et al. 2016

View full text Add to dashboard Cite

show abstract

“…One important advantage of using

H_{2}^{18} O

is that investigations of actively growing communities are not limited to amendments with simple substrates, but that growth on any substrate, including decaying plant litter, can be studied. Recent advances in SIP have enabled quantifying the growth of individual microbial taxa based on the degree to which they are labeled with 18 O (Hungate et al ., ). In this study, we show that quantitative stable isotope probing (qSIP; Hungate et al ., ) can be applied to aquatic ecosystems and identify actively growing aquatic bacteria during leaf litter decomposition.…”

Section: Introductionmentioning

confidence: 97%

“…Recent advances in SIP have enabled quantifying the growth of individual microbial taxa based on the degree to which they are labeled with 18 O (Hungate et al ., ). In this study, we show that quantitative stable isotope probing (qSIP; Hungate et al ., ) can be applied to aquatic ecosystems and identify actively growing aquatic bacteria during leaf litter decomposition.…”

Section: Introductionmentioning

confidence: 97%

Identification of growing bacteria during litter decomposition in freshwater through quantitative stable isotope probing

Hayer

Schwartz

Marks

et al. 2016

Environ Microbiol Rep

Self Cite

View full text Add to dashboard Cite

Identification of microorganisms that facilitate the cycling of nutrients in freshwater is paramount to understanding how these ecosystems function. Here, we identify growing aquatic bacteria using H218O quantitative stable isotope probing. During 8 day incubations in 97 atom % H218O, 54% of the taxa grew. The most abundant phyla among growing taxa were Proteobacteria (45%), Bacteroidetes (30%) and Firmicutes (10%). Taxa differed in isotopic enrichment, reflecting variation in DNA replication of bacterial populations. At the class level, the highest atom fraction excess was observed for OPB41 and δ-Proteobacteria. There was no linear relationship between O incorporation and abundance of taxa. δ-Proteobacteria and OPB41 were not abundant, yet the DNA of both taxa was highly enriched in O. Bacteriodetes, in contrast, were abundant but not highly enriched. Our study shows that a large proportion of the bacterial taxa found on decomposing leaf litter grew slowly, and several low abundance taxa were highly enriched. These findings indicating that rare organisms may be important for the decomposition of leaf litter in streams, and that quantitative stable isotope probing with H218O can be used to advance our understanding of microorganisms in freshwater by identifying species that are growing in complex communities.

show abstract

“…It partly enhances our understanding of how individual microbial taxa affect ecosystem processes like element cycling by analyzing microbial diversity of intact assemblages. However, it is a qualitative technique capable of identifying some of the organisms that utilize a substrate, not a quantitative one capable of exploring the full range of variation in isotope incorporation among microbial taxa [13]. NanoSIMS in combination with stable isotope probing was applied to analyze and image biological samples, which helps us better understand biological processes happening in complex systems.…”

Section: Introductionmentioning

confidence: 99%

Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies

et al. 2018

View full text Add to dashboard Cite

It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges.

show abstract

Quantitative Microbial Ecology through Stable Isotope Probing

Cited by 258 publications

References 66 publications

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

Identification of growing bacteria during litter decomposition in freshwater through quantitative stable isotope probing

Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies

Contact Info

Product

Resources

About