scholarly journals One step towards bioremediating a heavily polluted river: Metagenomic insights on the function of microbial community

2019 ◽  
Author(s):  
Luz Breton-Deval ◽  
Ayixon Sanchez-Reyes ◽  
Alejandro Sánchez-Flores ◽  
Katy Juárez ◽  
Patricia Mussali-Galante
Keyword(s):  
Microbial Community ◽  
Broad Spectrum ◽  
Water Samples ◽  
Shotgun Sequencing ◽  
Metabolic Potential ◽  
Polluted River ◽  
Future Design ◽  
Functional Potential ◽  
One Step ◽  
Bioremediation Processes

ABSTRACTThe objective of this study is to understand the functional potential of the microbial community related to bioremediation activity and its relationship with the pollution of each site to enhance the future design of more accurate bioremediation processes. Water samples were collected at four sampling sites along the Apatlaco River (S1-S4), and a whole metagenome shotgun sequencing was performed to know and understand the microbial community involved in bioremediation. Additionally, HMMER was used for searching sequence homologs related to PET and polystyrene biodegradation and metal transformation in Apatlaco River metagenomes. The Apatlaco River is characterized by the presence of a broad spectrum of microorganisms with the metabolic potential to carry out bioremediation activities. Every site along the Apatlaco River has a particular community to perform bioremediation activities. The first site S1 has Thiomonas, Polaromonas, Pedobacter, and Myroides, S2 has Pedobacter, Myroides, Pseudomonas and Acinetobacter, S3, Thiomonas, Myroides, Pseudomonas, Acinetobacter and Aeromonas; S4, Thiomonas, Myroides and Pseudomonas, Thauera.Furthermore, every site is rich in specific enzymes such as S1 has dioxygenase and dehydrogenase, which can degrade Catechol, Biphenyl, Naphthalene, and Phthalate. While, S2 and S3 are rich in dioxygenase and decarboxylating dehydrogenases to degrade Toluene, Fluorobenzoate, Xylene, Phenylpropanoate, and Phenol. S3 also has monooxygenases which degrade Benzene, and all the earlier mentioned enzymes were also found at S4.

scholarly journals CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

2021 ◽  
Vol 9 (4) ◽  
pp. 816
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
E. Luke McCarthy ◽  
Sean M. Hemmingsen ◽  
Edward Topp ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Shotgun Sequencing ◽  
Natural Ecosystems ◽  
Gene Markers ◽  
Microbial Profile ◽  
Microbial Ecosystems ◽  
Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

scholarly journals Reduced metagenome sequencing for strain-resolution taxonomic profiles

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Lars Snipen ◽  
Inga-Leena Angell ◽  
Torbjørn Rognes ◽  
Knut Rudi
Keyword(s):  
Microbial Community ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Good Alternative ◽  
Shotgun Sequencing ◽  
Least Square ◽  
Full Potential ◽  
Shotgun Metagenomics ◽  
Metagenome Sequencing ◽  
Reference Genomes

Abstract Background Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data. Results We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time. Conclusion We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS.

scholarly journals Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing

PLoS ONE ◽  
2016 ◽  
Vol 11 (2) ◽  
pp. e0149564 ◽  
Author(s):  
Sandrine Louis ◽  
Rewati-Mukund Tappu ◽  
Antje Damms-Machado ◽  
Daniel H. Huson ◽  
Stephan C. Bischoff
Keyword(s):  
Weight Loss ◽  
Microbial Community ◽  
Shotgun Sequencing ◽  
Obese Patients ◽  
Weight Loss Intervention ◽  
Gut Microbial Community

scholarly journals Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing

2020 ◽  
Author(s):  
Kimothy L Smith ◽  
Howard A Shuman ◽  
Douglas Findeisen
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Water Samples ◽  
Ad Hoc ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
The Other ◽  
Water Usage ◽  
16S Rrna Amplicon Sequencing ◽  
Oxford Nanopore

AbstractWe conducted two studies of water samples from buildings with normal occupancy and water usage compared to water from buildings that were unoccupied with little or no water usage due to the COVID-19 shutdown. Study 1 had 52 water samples obtained ad hoc from buildings in four metropolitan locations in different states in the US and a range of building types. Study 2 had 36 water samples obtained from two buildings in one metropolitan location with matched water sample types. One of the buildings had been continuously occupied, and the other substantially vacant for approximately 3 months. All water samples were analyzed using 16S rRNA amplicon sequencing with a MinION from Oxford Nanopore Technologies. More than 127 genera of bacteria were identified, including genera with members that are known to include more than 50 putative frank and opportunistic pathogens. While specific results varied among sample locations, 16S rRNA amplicon abundance and the diversity of bacteria were higher in water samples from unoccupied buildings than normally occupied buildings as was the abundance of sequenced amplicons of genera known to include pathogenic bacterial members. In both studies Legionella amplicon abundance was relatively small compared to the abundance of the other bacteria in the samples. Indeed, when present, the relative abundance of Legionella amplicons was lower in samples from unoccupied buildings. Legionella did not predominate in any of the water samples and were found, on average, in 9.6% of samples in Study 1 and 8.3% of samples in Study 2.SynopsisComparison of microbial community composition in the plumbing of occupied and unoccupied buildings during the COVID-19 pandemic shutdown.

scholarly journals New insights into the influence of plant and microbial diversity on denitrification rates in a salt marsh

2020 ◽  
Author(s):  
Olivia U. Mason ◽  
Patrick Chanton ◽  
Loren N. Knobbe ◽  
Julian Zaugg ◽  
Behzad Mortazavi
Keyword(s):  
Microbial Community ◽  
Salt Marsh ◽  
Microbial Diversity ◽  
Ecosystem Functions ◽  
Juncus Roemerianus ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Marsh Vegetation ◽  
Core Microbiome ◽  
N Removal

AbstractCoastal salt marshes are some of the most productive ecosystems on Earth, providing numerous services such as soil carbon storage, flood protection and nutrient filtering, several of which are mediated by the sediment microbiome associated with marsh vegetation. Here, nutrient filtering (nitrate removal through denitrification) was examined by determining microbial community structure (16S rRNA gene iTag sequencing), diversity, denitrification rates and metabolic potential (assembled metagenomic sequences) in collocated patches of Spartina alterniflora (Spartina) and Juncus roemerianus (Juncus) sediments. The iTag data showed that diversity and richness in Spartina and Juncus sediment microbial communities were highly similar. However, microbial community evenness differed significantly, with the most even communities observed in Juncus sediments. Further, denitrification rates were significantly higher in Juncus compared to Spartina, suggesting oscillations in microbial abundances and in particular the core microbiome identified herein, along with plant diversity influence marsh nitrogen (N) removal. Amplicon and assembled metagenome sequences pointed to a potentially important, yet unappreciated Planctomycetes role in N removal in the salt marsh. Thus, perturbations, such as sea-level rise, that can alter marsh vegetation distribution could impact microbial diversity and may ultimately influence the ecologically important ecosystem functions the marsh sediment microbiome provides.

scholarly journals Geothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, Italy

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Nunzia Picone ◽  
Carmen Hogendoorn ◽  
Geert Cremers ◽  
Lianna Poghosyan ◽  
Arjan Pol ◽  
...  
Keyword(s):  
Microbial Community ◽  
Greenhouse Gas ◽  
Relative Abundance ◽  
Hot Spots ◽  
Microbial Community Composition ◽  
Metagenomic Analysis ◽  
Volcanic Soil ◽  
Metabolic Potential ◽  
Gas Emissions ◽  
Geothermal Activity

ABSTRACT Volcanic and geothermal environments are characterized by low pH, high temperatures, and gas emissions consisting of mainly CO2 and varied CH4, H2S, and H2 contents which allow the formation of chemolithoautotrophic microbial communities. To determine the link between the emitted gases and the microbial community composition, geochemical and metagenomic analysis were performed. Soil samples of the geothermic region Favara Grande (Pantelleria, Italy) were taken at various depths (1 to 50 cm). Analysis of the gas composition revealed that CH4 and H2 have the potential to serve as the driving forces for the microbial community. Our metagenomic analysis revealed a high relative abundance of Bacteria in the top layer (1 to 10 cm), but the relative abundance of Archaea increased with depth from 32% to 70%. In particular, a putative hydrogenotrophic methanogenic archaeon, related to Methanocella conradii, appeared to have a high relative abundance (63%) in deeper layers. A variety of [NiFe]-hydrogenase genes were detected, showing that H2 was an important electron donor for microaerobic microorganisms in the upper layers. Furthermore, the bacterial population included verrucomicrobial and proteobacterial methanotrophs, the former showing an up to 7.8 times higher relative abundance. Analysis of the metabolic potential of this microbial community showed a clear capacity to oxidize CH4 aerobically, as several genes for distinct particulate methane monooxygenases and lanthanide-dependent methanol dehydrogenases (XoxF-type) were retrieved. Analysis of the CO2 fixation pathways showed the presence of the Calvin-Benson-Bassham cycle, the Wood-Ljungdahl pathway, and the (reverse) tricarboxylic acid (TCA) cycle, the latter being the most represented carbon fixation pathway. This study indicates that the methane emissions in the Favara Grande might be a combination of geothermal activity and biological processes and further provides insights into the diversity of the microbial population thriving on CH4 and H2. IMPORTANCE The Favara Grande nature reserve on the volcanic island of Pantelleria (Italy) is known for its geothermal gas emissions and high soil temperatures. These volcanic soil ecosystems represent “hot spots” of greenhouse gas emissions. The unique community might be shaped by the hostile conditions in the ecosystem, and it is involved in the cycling of elements such as carbon, hydrogen, sulfur, and nitrogen. Our metagenome study revealed that most of the microorganisms in this extreme environment are only distantly related to cultivated bacteria. The results obtained profoundly increased the understanding of these natural hot spots of greenhouse gas production/degradation and will help to enrich and isolate the microbial key players. After isolation, it will become possible to unravel the molecular mechanisms by which they adapt to extreme (thermo/acidophilic) conditions, and this may lead to new green enzymatic catalysts and technologies for industry.

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