16-s.org 16s rRNA Sequencing: The Fabric of Metagenomics

Appl Environ Microbiol. 2016 Jul 15;82(15):4470-81. doi: 10.1128/AEM.00902-16. Print 2016 Aug 1.

Influence of Fishmeal-Free Diets on Microbial Communities in Atlantic Salmon (Salmo salar) Recirculation Aquaculture Systems.

Schmidt V1, Amaral-Zettler L2, Davidson J3, Summerfelt S3, Good C4.

Author information


Reliance on fishmeal as a primary protein source is among the chief economic and environmental concerns in aquaculture today. Fishmeal-based feeds often require harvest from wild fish stocks, placing pressure on natural ecosystems and causing price instability. Alternative diet formulations without the use of fishmeal provide a potential solution to this challenge. Although the impact of alternative diets on fish performance, intestinal inflammation, palatability, and gut microbiota has been a topic of recent interest, less is known about how alternative feeds impact the aquaculture environment as a whole. The recent focus on recirculating aquaculture systems (RAS) and the closed-containment approach to raising food fish highlights the need to maintain stable environmental and microbiological conditions within a farm environment. Microbial stability in RAS biofilters is particularly important, given its role in nutrient processing and water quality in these closed systems. If and how the impacts of alternative feeds on microbial communities in fish translate into changes to the biofilters are not known. We tested the influence of a fishmeal-free diet on the microbial communities in RAS water, biofilters, and salmon microbiomes using high-throughput 16S rRNA gene V6 hypervariable region amplicon sequencing. We grew Atlantic salmon (Salmo salar) to market size in six replicate RAS tanks, three with traditional fishmeal diets and three with alternative-protein, fishmeal-free diets. We sampled intestines and gills from market-ready adult fish, water, and biofilter medium in each corresponding RAS unit. Our results provide data on how fish diet influences the RAS environment and corroborate previous findings that diet has a clear influence on the microbiome structure of the salmon intestine, particularly within the order Lactobacillales (lactic acid bacteria). We conclude that the strong stability of taxa likely involved in water quality processing regardless of diet (e.g., Nitrospira) may further alleviate concerns regarding the use of alternative feeds in RAS operations.


The growth of the aquaculture industry has outpaced terrestrial livestock production and wild-capture fisheries for over 2 decades, currently producing nearly 50% of all seafood consumed globally. As wild-capture fisheries continue to decline, aquaculture's role in food production will grow, and it will produce an estimated 62% of all seafood consumed in 2020. A significant environmental concern of the industry is the reliance on fishmeal as a primary feed ingredient, as its production still requires harvest from wild fisheries. Our study adds to the growing body of literature on the feasibility of alternative, fishmeal-free diets. Specifically, we asked how fishmeal-free diets influence microbial communities in recirculating salmon farms. Unlike previous studies, we extended our investigation beyond the microbiome of the fish itself and asked how alterative diets influence microbial communities in water and critical biofilter habitats. We found no evidence for adverse effects of alternative diets on any microbial habitat within the farm.

Copyright © 2016 Schmidt et al.

PMID: 27129964 PMCID: PMC4984271 DOI: 10.1128/AEM.00902-16

[PubMed - in process] Free PMC Article

Similar articles

Icon for HighWireIcon for PubMed Central

Select item 27120417



Environ Microbiol Rep. 2016 Apr 27. doi: 10.1111/1758-2229.12418. [Epub ahead of print]

The effects of host age and spatial location on bacterial community composition in the English Oak tree (Quercus robur).

Meaden S1, Metcalf CJ2,3, Koskella B4.

Author information


Drivers of bacterial community assemblages associated with plants are diverse and include biotic factors, such as competitors and host traits, and abiotic factors, including environmental conditions and dispersal mechanisms. We examine the roles of spatial distribution and host size, as an approximation for age, in shaping the microbiome associated with Quercus robur woody tissue using culture-independent 16S rRNA gene amplicon sequencing. In addition to providing a baseline survey of the Q. robur microbiome, we screened for the pathogen of acute oak decline. Our results suggest that age is a predictor of bacterial community composition, demonstrating a surprising negative correlation between tree age and alpha diversity. We find no signature of dispersal limitation within the Wytham Woods plot sampled. Together, these results provide evidence for niche-based hypotheses of community assembly and the importance of tree age in bacterial community structure, as well as highlighting that caution must be applied when diagnosing dysbiosis in a long-lived plant host.

© 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

PMID: 27120417 DOI: 10.1111/1758-2229.12418

[PubMed - as supplied by publisher]

Similar articles

Icon for Wiley

Select item 27118012



Appl Microbiol Biotechnol. 2016 Aug;100(16):7297-309. doi: 10.1007/s00253-016-7559-8. Epub 2016 Apr 27.

Microbial community characterization and functional gene quantification in RDX-degrading microcosms derived from sediment and groundwater at two naval sites.

Wilson FP1, Cupples AM2.

Author information


The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has long been recognized as a problematic environmental pollutant, and efforts to remediate contaminated soils, sediments, and groundwater have been going on for decades. In recent years, much interest has focused on using bioremediation to clean up these sites. The current study investigated the microorganisms (16S rRNA genes, Illumina) and functional genes (xenA, xenB, and xplA) linked to RDX biodegradation in microcosms composed of sediment or groundwater from two Navy sites. For this, experiments included sediment samples from three depths (5 to 30 ft) from two wells located in one Navy site. In addition, the groundwater upstream and downstream of an emulsified oil biobarrier was examined from another Navy site. Further, for the groundwater experiments, the effect of glucose addition was explored. For the sediment experiments, the most enriched phylotypes during RDX degradation varied over time, by depth and well locations. However, several trends were noted, including the enrichment of Pseudomonas, Rhodococcus, Arthrobacter, and Sporolactobacillus in the sediment microcosms. For the groundwater-based experiments, Pseudomonas, unclassified Rhodocyclaceae, Sphingomonas, and Rhodococcus were also highly abundant during RDX degradation. The abundance of both xplA and xenA significantly increased during RDX degradation compared to the control microcosms for many treatments (both groundwater and sediment microcosms). In a limited number of microcosms, the copy number of the xenB gene increased. Phylotype data were correlated with functional gene data to highlight potentially important biomarkers for RDX biodegradation at these two Navy sites.


High-throughput amplicon sequencing; RDX; xenA; xenB; xplA

PMID: 27118012 DOI: 10.1007/s00253-016-7559-8

[PubMed - in process]

Similar articles

Icon for Springer

Select item 27112927



Arch Microbiol. 2016 Aug;198(6):591-4. doi: 10.1007/s00203-016-1228-2. Epub 2016 Apr 25.

Targeting single-nucleotide polymorphisms in the 16S rRNA gene to detect and differentiate Legionella pneumophila and non-Legionella pneumophila species.

Zhan XY1,2,3, Hu CH1,2, Zhu QY4,5.

Author information


A PCR-based method targeting single-nucleotide polymorphisms (SNPs) in the 16S rRNA gene was developed for differential identification of Legionella pneumophila and non-Legionella pneumophila. Based on the bioinformatics analysis for 176 Legionella 16S rRNA gene fragments of 56 different Legionella species, a set of SNPs, A(628)C(629) was found to be highly specific to L. pneumophila strains. A multiplex assay was designed that was able to distinguish sites with limited sequence heterogeneity between L. pneumophila and non-L. pneumophila in the targeted 16S rRNA gene. The assay amplified a 261-bp amplicon for Legionella spp. and a set of 203- and 97-bp amplicons only specific to L. pneumophila species. Among 49 ATCC strains and 284 Legionella isolates from environmental water and clinical samples, 100 % of L. pneumophila and non-L. pneumophila strains were correctly identified and differentiated by this assay. The assay presents a more rapid, sensitive and alternative method to the currently available PCR-sequencing detection and differentiation method.


16S rRN


The Ion Proton is Just One of Our Many NGS Platforms. Contact Us To See Which Platform Best Fits Your Needs