scholarly journals Trophic Selective Pressures Organize the Composition of Endolithic Microbial Communities from Global Deserts

2019 ◽  
Author(s):  
Evan Qu ◽  
Chris Omelon ◽  
Aharon Oren ◽  
Victoria Meslier ◽  
Don A. Cowan ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
Community Assembly ◽  
High Throughput Sequencing ◽  
Regional Scale ◽  
Marker Gene ◽  
Trophic Levels ◽  
Striking Difference ◽  
Climate Conditions ◽  
Endolithic Community

AbstractStudies of microbial biogeography are often convoluted by extremely high diversity and differences in microenvironmental factors such as pH and nutrient availability. Desert endolithic (inside rock) communities are exceptionally simple ecosystems that can serve as a tractable model for investigating long-range biogeographic effects on microbial communities. We conducted a comprehensive survey of endolithic sandstones using high-throughput marker gene sequencing to characterize global patterns of diversity in endolithic microbial communities. We also tested a range of abiotic variables in order to investigate the factors that drive community assembly at various trophic levels. Macroclimate was found to be the primary driver of endolithic community composition, with the most striking difference witnessed between hot and polar deserts. This difference was largely attributable to the specialization of prokaryotic and eukaryotic primary producers to different climate conditions. On a regional scale, microclimate and properties of the rock substrate were found to influence community assembly, although to a lesser degree than global hot versus polar conditions. We found new evidence that the factors driving endolithic community assembly differ between trophic levels. While phototrophic taxa were rigorously selected for among different sites, heterotrophic taxa were more cosmopolitan, suggesting that stochasticity plays a larger role in heterotroph assembly. This study is the first to uncover the global drivers of desert endolithic diversity using high-throughput sequencing. We demonstrate that phototrophs and heterotrophs in the endolithic community assemble under different stochastic and deterministic influences, emphasizing the need for studies of microorganisms in context of their functional niche in the community.

scholarly journals Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 241-252
Author(s):  
Dyah Asri Handayani Taroepratjeka ◽  
Tsuyoshi Imai ◽  
Prapaipid Chairattanamanokorn ◽  
Alissara Reungsang
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
High Salinity ◽  
Amplicon Sequencing ◽  
Spatial Proximity ◽  
Lignocellulosic Waste ◽  
Evaporation Pond ◽  
Operational Taxonomic Units ◽  
Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

scholarly journals Novel Approach to Study the Diversity of Soil Microbial Communities in Qatar

2020 ◽  
Author(s):  
Jane Oja ◽  
Sakeenah Adenan ◽  
Abdel-Fattah Talaat ◽  
Juha Alatalo
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
Mycorrhizal Fungi ◽  
High Throughput Sequencing ◽  
Soil Microbial Communities ◽  
Arbuscular Mycorrhizal ◽  
Soil Microbial ◽  
Fungal Abundance ◽  
Novel Approach ◽  
Soil Climate

A broad diversity of microorganisms can be found in soil, where they are essential for nutrient cycling and energy transfer. Recent high-throughput sequencing methods have greatly advanced our knowledge about how soil, climate and vegetation variables structure the composition of microbial communities in many world regions. However, we are lacking information from several regions in the world, e.g. Middle-East. We have collected soil from 19 different habitat types for studying the diversity and composition of soil microbial communities (both fungi and bacteria) in Qatar and determining which edaphic parameters exert the strongest influences on these communities. Preliminary results indicate that in overall bacteria are more abundant in soil than fungi and few sites have notably higher abundance of these microbes. In addition, we have detected some soil patameters, which tend to have reduced the overall fungal abundance and enhanced the presence of arbuscular mycorrhizal fungi and N-fixing bacteria. More detailed information on the diversity and composition of soil microbial communities is expected from the high-throughput sequenced data.

Comparison of two high throughput sequencing platforms for the identification of microbial communities of historical funeral accessories

2019 ◽  
Vol 305 ◽  
pp. S44
Author(s):  
K. Soltys ◽  
K. Soltys ◽  
M. Plany ◽  
Z. Kisova ◽  
A. Puskarova ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequencing Platforms

scholarly journals High Throughput Sequencing and Network Analysis Disentangle the Microbial Communities of Ticks and Hosts Within and Between Ecosystems

2018 ◽  
Vol 8 ◽  
Author(s):  
Agustín Estrada-Peña ◽  
Alejandro Cabezas-Cruz ◽  
Thomas Pollet ◽  
Muriel Vayssier-Taussat ◽  
Jean-François Cosson
Keyword(s):  
Network Analysis ◽  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing

High-throughput sequencing of microbial communities in Poro cheese, an artisanal Mexican cheese

2014 ◽  
Vol 44 ◽  
pp. 136-141 ◽  
Author(s):  
Alejandro Aldrete-Tapia ◽  
Meyli C. Escobar-Ramírez ◽  
Mark L. Tamplin ◽  
Montserrat Hernández-Iturriaga
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing

scholarly journals Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing

2016 ◽  
Vol 82 (24) ◽  
pp. 7217-7226 ◽  
Author(s):  
D. Lee Taylor ◽  
William A. Walters ◽  
Niall J. Lennon ◽  
James Bochicchio ◽  
Andrew Krohn ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Large Subunit ◽  
Marker Gene ◽  
Soil Samples ◽  
Gene Copy ◽  
Accurate Estimation ◽  
Rrna Gene ◽  
Data Set ◽  
Mock Communities

ABSTRACTWhile high-throughput sequencing methods are revolutionizing fungal ecology, recovering accurate estimates of species richness and abundance has proven elusive. We sought to design internal transcribed spacer (ITS) primers and an Illumina protocol that would maximize coverage of the kingdom Fungi while minimizing nontarget eukaryotes. We inspected alignments of the 5.8S and large subunit (LSU) ribosomal genes and evaluated potential primers using PrimerProspector. We tested the resulting primers using tiered-abundance mock communities and five previously characterized soil samples. We recovered operational taxonomic units (OTUs) belonging to all 8 members in both mock communities, despite DNA abundances spanning 3 orders of magnitude. The expected and observed read counts were strongly correlated (r= 0.94 to 0.97). However, several taxa were consistently over- or underrepresented, likely due to variation in rRNA gene copy numbers. The Illumina data resulted in clustering of soil samples identical to that obtained with Sanger sequence clone library data using different primers. Furthermore, the two methods produced distance matrices with a Mantel correlation of 0.92. Nonfungal sequences comprised less than 0.5% of the soil data set, with most attributable to vascular plants. Our results suggest that high-throughput methods can produce fairly accurate estimates of fungal abundances in complex communities. Further improvements might be achieved through corrections for rRNA copy number and utilization of standardized mock communities.IMPORTANCEFungi play numerous important roles in the environment. Improvements in sequencing methods are providing revolutionary insights into fungal biodiversity, yet accurate estimates of the number of fungal species (i.e., richness) and their relative abundances in an environmental sample (e.g., soil, roots, water, etc.) remain difficult to obtain. We present improved methods for high-throughput Illumina sequencing of the species-diagnostic fungal ribosomal marker gene that improve the accuracy of richness and abundance estimates. The improvements include new PCR primers and library preparation, validation using a known mock community, and bioinformatic parameter tuning.

scholarly journals Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiota analysis

2019 ◽  
Author(s):  
Emilie Lejal ◽  
Agustín Estrada-Peña ◽  
Maud Marsot ◽  
Jean-François Cosson ◽  
Olivier Rué ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dna Extraction ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
Community Diversity ◽  
Analytical Process ◽  
Sequencing Technologies ◽  
And Gender ◽  
The Impact

AbstractBackgroundThe development of high throughput sequencing technologies has substantially improved analysis of bacterial community diversity, composition, and functions. Over the last decade, high throughput sequencing has been used extensively to identify the diversity and composition of tick microbial communities. However, a growing number of studies are warning about the impact of contamination brought along the different steps of the analytical process, from DNA extraction to amplification. In low biomass samples, e.g. individual tick samples, these contaminants may represent a large part of the obtained sequences, and thus generate considerable errors in downstream analyses and in the interpretation of results. Most studies of tick microbiota either do not mention the inclusion of controls during the DNA extraction or amplification steps, or consider the lack of an electrophoresis signal as an absence of contamination. In this context, we aimed to assess the proportion of contaminant sequences resulting from these steps. We analyzed the microbiota of individual Ixodes ricinus ticks by including several categories of controls throughout the analytical process: crushing, DNA extraction, and DNA amplification.ResultsControls yielded a significant number of sequences (1,126 to 13,198 mean sequences, depending on the control category). Some operational taxonomic units (OTUs) detected in these controls belong to genera reported in previous tick microbiota studies. In this study, these OTUs accounted for 50.9% of the total number of sequences in our samples, and were considered contaminants. Contamination levels (i.e. the percentage of sequences belonging to OTUs identified as contaminants) varied with tick stage and gender: 76.3% of nymphs and 75% of males demonstrated contamination over 50%, while most females (65.7%) had rates lower than 20%. Contamination mainly corresponded to OTUs detected in crushing and DNA extraction controls, highlighting the importance of carefully controlling these steps.ConclusionHere, we showed that contaminant OTUs from extraction and amplification steps can represent more than half the total sequence yield in sequencing runs, and lead to unreliable results when characterizing tick microbial communities. We thus strongly advise the routine use of negative controls in tick microbiota studies, and more generally in studies involving low biomass samples.

scholarly journals Comparative Analysis of the Gut Microbial Communities in Forest and Alpine Musk Deer Using High-Throughput Sequencing

2017 ◽  
Vol 8 ◽  
Author(s):  
Xiaolong Hu ◽  
Gang Liu ◽  
Aaron B. A. Shafer ◽  
Yuting Wei ◽  
Juntong Zhou ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Musk Deer
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