Effects of humic acid on pentachlorophenol biodegrading microorganisms elucidated by stable isotope probing and high-throughput sequencing approaches

2018 ◽  
Vol 69 (2) ◽  
pp. 380-391 ◽  
Author(s):  
H. Tong ◽  
M. J. Chen ◽  
F. B. Li ◽  
C. S. Liu ◽  
B. Li ◽  
...  
Keyword(s):  
Humic Acid ◽  
Stable Isotope ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Stable Isotope Probing

scholarly journals Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape

2017 ◽  
Vol 83 (22) ◽  
Author(s):  
Konstantia Gkarmiri ◽  
Shahid Mahmood ◽  
Alf Ekblad ◽  
Sadhna Alström ◽  
Nils Högberg ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Stable Isotope ◽  
Oilseed Rape ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Stable Isotope Probing ◽  
Biofuel Production ◽  
Content Type ◽  
Bacteria And Fungi

ABSTRACT RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following 13CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the 13C- and 12C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. “Candidatus Nitrososphaera” was enriched in 13C in rhizosphere soil. Olpidium and Dendryphion were abundant in the 12C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily 13C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was 13C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napus. IMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following 13CO2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.

scholarly journals Novel bacteria capable of degrading phenanthrene in activated sludge revealed by stable-isotope probing coupled with high-throughput sequencing

2017 ◽  
Vol 28 (5-6) ◽  
pp. 423-436 ◽  
Author(s):  
Jibing Li ◽  
Dayi Zhang ◽  
Mengke Song ◽  
Longfei Jiang ◽  
Yujie Wang ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Activated Sludge ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Stable Isotope Probing ◽  
Novel Bacteria

Ultra-high-sensitivity stable-isotope probing of rRNA by high-throughput sequencing of isopycnic centrifugation gradients

2015 ◽  
Vol 7 (2) ◽  
pp. 282-287 ◽  
Author(s):  
Tomo Aoyagi ◽  
Satoshi Hanada ◽  
Hideomi Itoh ◽  
Yuya Sato ◽  
Atsushi Ogata ◽  
...  
Keyword(s):  
Stable Isotope ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
High Sensitivity ◽  
Stable Isotope Probing ◽  
Isopycnic Centrifugation

scholarly journals HTSSIP: an R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments

2017 ◽  
Author(s):  
Nicholas D. Youngblut ◽  
Samuel E. Barnett ◽  
Daniel H. Buckley
Keyword(s):  
High Resolution ◽  
Stable Isotope ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
R Package ◽  
Stable Isotope Probing ◽  
Sequencing Data ◽  
Metabolic Processes ◽  
Link Type ◽  
High Throughput Sequencing Data

AbstractCombining high throughput sequencing with stable isotope probing (HTS-SIP) is a powerful method for mapping in situ metabolic processes to thousands of microbial taxa. However, accurately mapping metabolic processes to taxa is complex and challenging. Multiple HTS-SIP data analysis methods have been developed, including high-resolution stable isotope probing (HR-SIP), multi-window high-resolution stable isotope probing (MW-HR-SIP), quantitative stable isotope probing (q-SIP), and ΔBD. Currently, the computational tools to perform these analyses are either not publicly available or lack documentation, testing, and developer support. To address this shortfall, we have developed the HTSSIP R package, a toolset for conducting HTS-SIP analyses in a straightforward and easily reproducible manner. The HTSSIP package, along with full documentation and examples, is available from CRAN at https://cran.r-project.org/web/packages/HTSSIP/index.html and Github at https://github.com/nick-youngblut/HTSSIP.

scholarly journals Characteristics of Macroalgal Consumption by Eight Herbivorous Coral Reef Fishes From the Xisha Islands, China, as Determined by Microscopy, 18S rRNA High-throughput Sequencing and Stable Isotope Analyses

2021 ◽  
Author(s):  
Peng Wu ◽  
Teng Wang ◽  
Yong Liu ◽  
Chunhou Li ◽  
Yayuan Xiao ◽  
...  
Keyword(s):  
Coral Reef ◽  
Stable Isotope ◽  
Coral Reefs ◽  
High Throughput ◽  
Fish Species ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Xisha Islands ◽  
Herbivorous Fishes ◽  
Isotope Analyses

Abstract Herbivorous fishes play an important role in controlling the overabundance of macroalgae on coral reefs. Understanding the feeding selectivity and consumption of macroalgae by herbivorous fishes can be challenging in studies of their ecological role in the preservation and recovery of coral reefs. Coral reef decline, macroalgal overgrowth and overfishing are clearly visible in the Xisha Islands, China. However, there have been no studies of the feeding behaviors of herbivorous fishes in this area. We used microscopy, 18S rRNA high-throughput sequencing and stable isotope analyses to comprehensively examine the dietary spectrum of eight herbivorous reef fish species common in the Xisha Islands, including one parrotfish, two chub, two unicorn fish and three rabbitfish. Multi-technique analyses of intestinal contents revealed that Kyphosus vaigiensis, Naso unicornis and Siganus argenteus showed a high consumption potential of macroalgae, suggesting that they are the key browsers which should receive priority protection in in the Xisha Islands. Kyphosus cinerascens, K. vaigiensis, N. unicornis and S. punctatissimus fed on the entire macroalgal thallus, indicating their greater ecological importance compared with species which only consume the algal fronds. However, Calotomus carolinus can consume the red alga Pneophyllum conicum, which is widely distributed on Indo-Pacific coral reefs and can overgrow and kill live corals. Clearly, a diverse herbivorous fish fauna is very important in the Xisha coral reefs. These results not only demonstrated the various functions of different herbivorous fish species in macroalgal removal, but also provided insights into the management of herbivorous fishes on the coral reefs of the South China Sea.

DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms

2016 ◽  
pp. 57-74 ◽  
Author(s):  
Eleanor Jameson ◽  
Martin Taubert ◽  
Sara Coyotzi ◽  
Yin Chen ◽  
Özge Eyice ◽  
...  
Keyword(s):  
Stable Isotope ◽  
High Throughput ◽  
Stable Isotope Probing ◽  
Biomarker Analysis
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