scholarly journals Biogeography and Biodiversity in Sulfide Structures of Active and Inactive Vents at Deep-Sea Hydrothermal Fields of the Southern Mariana Trough

2010 ◽  
Vol 76 (9) ◽  
pp. 2968-2979 ◽  
Author(s):  
Shingo Kato ◽  
Yoshinori Takano ◽  
Takeshi Kakegawa ◽  
Hironori Oba ◽  
Kazuhiko Inoue ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Organic Content ◽  
Hyperthermophilic Archaea ◽  
Spreading Center ◽  
Rrna Gene ◽  
Hydrothermal Fields

ABSTRACT The abundance, diversity, activity, and composition of microbial communities in sulfide structures both of active and inactive vents were investigated by culture-independent methods. These sulfide structures were collected at four hydrothermal fields, both on- and off-axis of the back-arc spreading center of the Southern Mariana Trough. The microbial abundance and activity in the samples were determined by analyzing total organic content, enzymatic activity, and copy number of the 16S rRNA gene. To assess the diversity and composition of the microbial communities, 16S rRNA gene clone libraries including bacterial and archaeal phylotypes were constructed from the sulfide structures. Despite the differences in the geological settings among the sampling points, phylotypes related to the Epsilonproteobacteria and cultured hyperthermophilic archaea were abundant in the libraries from the samples of active vents. In contrast, the relative abundance of these phylotypes was extremely low in the libraries from the samples of inactive vents. These results suggest that the composition of microbial communities within sulfide structures dramatically changes depending on the degree of hydrothermal activity, which was supported by statistical analyses. Comparative analyses suggest that the abundance, activity and diversity of microbial communities within sulfide structures of inactive vents are likely to be comparable to or higher than those in active vent structures, even though the microbial community composition is different between these two types of vents. The microbial community compositions in the sulfide structures of inactive vents were similar to those in seafloor basaltic rocks rather than those in marine sediments or the sulfide structures of active vents, suggesting that the microbial community compositions on the seafloor may be constrained by the available energy sources. Our findings provide helpful information for understanding the biogeography, biodiversity and microbial ecosystems in marine environments.

scholarly journals Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Alexander Burkert ◽  
Thomas A. Douglas ◽  
Mark P. Waldrop ◽  
Rachel Mackelprang
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Subzero Temperatures ◽  
Dormant Cells

ABSTRACTPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the classBacilliwere more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of theClostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCEPermafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

scholarly journals Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence

2018 ◽  
Author(s):  
Alex Burkert ◽  
Thomas A. Douglas ◽  
Mark P. Waldrop ◽  
Rachel Mackelprang
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Subzero Temperatures ◽  
Dormant Cells

AbstractPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods such as metagenomic and 16S rRNA gene sequencing. However, these methods do not distinguish between active, dead, and dormant cells. This is of particular concern in ancient permafrost where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this we applied: (i) live/dead differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19K, 27K, and 33K). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools and how they change over geologic time. We found clear evidence that cells capable of forming endospores are not necessarily dormant and that the propensity to form endospores differed among taxa. Specifically, Bacilli are more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of Clostridia, which are more likely to persist as vegetative cells over geologic timescales. We also found that exogenous DNA preserved within permafrost does not bias DNA sequencing results since its removal did not significantly alter the microbial community composition. These results extend the findings of a previous study that showed permafrost age and ice content largely control microbial community diversity and cell abundances.ImportanceThe study of permafrost transcends the study of climate change and exobiology. Permafrost soils store more than half earth’s soil carbon despite covering ∽15% of the land area (Tarnocai et al 2009). This permafrost carbon is rapidly degraded following thaw (Tarnocai C et al 2009, Schuur et al 2015). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling post thaw. Permafrost is also an analog for frozen extraterrestrial environments and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive permafrost we can focus efforts searching for evidence of life on cryogenic cosmic bodies. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains across geologic timescales.

Organotrophic and Mixotrofic Sulfur Oxidation in an Acidic Salt Flat in Northern Chile

2015 ◽  
Vol 1130 ◽  
pp. 63-66 ◽  
Author(s):  
Lorena Escudero ◽  
Jonathan Bijman ◽  
Guajardo M. Mariela ◽  
Juan José Pueyo Mur ◽  
Guillermo Chong ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Composition ◽  
Iron Concentration ◽  
Rrna Gene ◽  
Salt Flat ◽  
Significant Difference ◽  
Acidic Salt ◽  
The 16S Rrna Gene

To understand the microbial community inhabiting in an acidic salt flat the phylogenetic diversity and the geochemistry of this system was compared to acid mine drainage (AMD) systems. The microbial community structure was assessed by DNA extraction/PCR/DGGE and secuencing for the 16S rRNA gene and the geochemistry was analyzed using several approaches. Prediction of metagenome functional content was performed from the 16S rRNA gene survey using the bioinformatics software package Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). The geochemical results revealed a much lower iron concentration in the salt flat than in AMD systems (39 and 21804 mg L-1, respectively) and a significant difference in chloride levels. Sequences inferred to be from potential sulfur metabolizing organisms constituted up to 70% of the microbial community in the acidic salt flat meanwhile predominat iron-metabolizing acidophile populations were reported in AMD systems. Interestingly, the microbial assemblage in the acidic salt flat was dominated by mixotrophic and organotrophic sulfur oxidizers as well as by photoautotrophic acidophiles. Our results suggests that the salt concentration in Salar de Gorbea (average Cl-= 40 gL-1) is in the limit for the occurrence of chemolithotrophic oxidation of sulfur compounds. In addition, the investigation allows concluding that salinity rather than extremes of pH is the major environmental determinant of microbial community composition.

scholarly journals 16S rRNA Gene Amplicon Sequencing of Microbial Communities Involved in Anaerobic Bulking in a Mesophilic Expanded Granular Sludge Bed Reactor Treating Wastewater Discharged from a Japanese-Style Thickened Worcestershire Sauce-Producing Factory

2019 ◽  
Vol 8 (36) ◽  
Author(s):  
Takeshi Yamada ◽  
Jun Harada ◽  
Yuki Okazaki ◽  
Tsuyoshi Yamaguchi ◽  
Atsushi Nakano
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Granular Sludge ◽  
Amplicon Sequencing ◽  
Organic Content ◽  
Rrna Gene ◽  
Sludge Bulking ◽  
High Organic Content

We analyzed the prokaryotes in bulking and healthy sludge from a mesophilic expanded granular sludge bed reactor treating wastewater with high organic content by 16S rRNA gene amplicon sequencing. We tabulated the microbiota at the phylum level, providing a framework for avoiding sludge bulking.

scholarly journals TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution

mSphere ◽  
2018 ◽  
Vol 3 (5) ◽  
Author(s):  
Robin R. Rohwer ◽  
Joshua J. Hamilton ◽  
Ryan J. Newton ◽  
Katherine D. McMahon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Data Sets ◽  
Data Set ◽  
Comprehensive Database ◽  
Fine Resolution

ABSTRACT Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set’s sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source and is available at https://www.github.com/McMahonLab/TaxAss. IMPORTANCE Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are data set dependent and cannot be compared between data sets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus, and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between data sets.

scholarly journals Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform

PLoS ONE ◽  
2015 ◽  
Vol 10 (2) ◽  
pp. e0116955 ◽  
Author(s):  
Lucas Sinclair ◽  
Omneya Ahmed Osman ◽  
Stefan Bertilsson ◽  
Alexander Eiler
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Illumina Platform

scholarly journals Distribution of Acetothermia-dominated microbial communities in alkaline hot springs of Baikal Rift Zone.

2017 ◽  
Author(s):  
Svetlana V. Zaitseva ◽  
Elena V. Lavrentieva ◽  
Aryuna A. Radnagurueva ◽  
Olga A. Baturina ◽  
Marsel R. Kabilov ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Hot Springs ◽  
Rift Zone ◽  
Hot Spring ◽  
Baikal Rift Zone ◽  
Rrna Gene ◽  
Acetyl Coa Pathway

Alkaline hot springs are unique extreme habitats resemble the early Earth and present a valuable resource for the discovery of procaryotic community diversity and isolation of the novel thermophilic Bacteria and Archaea. One of the model for the possible origin of biochemistry in alkaline hot springs revealed the acetyl-CoA pathway of CO2 fixation might be the most ancient form of carbon metabolism. Recent phylogenetic studies have suggested that the phylum Acetothermia is one of the deep branches of the Bacteria domain. Firstly Acetothermia (Candidate division OP1) was characterized in a culture independent molecular phylogenetic survey based on the 16S rRNA gene of the sulfide-rich hot spring, Obsidian Pool, a 75 to 95oC hot spring. Two nearly complete genomes of Acetothermia were established based on genome-resolved metagenomic analysis and its capability of implementing acetogenesis through the ancient reductive acetyl-CoA pathway by utilizing CO2 and H2 was revealed. Although genomic, proteomic and metagenomic approaches investigate basic metabolism and potentional energy conservation of uncultivated candidate phyla but ecological roles of these bacteria and general patterns of diversity and community structure stay unclear. General hydrochemical and geological characterization of alkaline thermal springs of the Baikal Rift zone with high silica concentrations and a nitrogen dominated gas phase is provided. Previous microbiogical studies based on culture-dependent methods recovered a large number of bacterial strains from thermal springs located in Baikal Rift zone. We combined microbial communities analysis by using high-throughput 16S rRNA gene sequencing, biogeochemical measurements, sediment mineralogy and physicochemical characteristics to investigate ecosystems of alkaline hot springs located in the Baikal Rift zone. Uncultivated bacteria belonging to the phylum Acetothermia, along with members of the phyla Firmicutes and Proteobacteria, were identified as the dominant group in hydrothermal sediments communities in the alkaline hot springs of Baikal Rift zone. In bottom sediments of the Alla hot spring, about 57% of all classified sequences represent this phylum. Geochemistry of fluids and sample type were strongly correlated with microbial community composition. The Acetothermia exhibited the highest relative abundance in sediment microbial community associated with alkaline thermal fluids enriched in Fe, Zn, Ni, Al and Cr.

scholarly journals Dead or Alive? Molecular life-dead distinction in human stool samples reveals significantly different composition of the microbial community

2018 ◽  
Author(s):  
Alexandra Perras ◽  
Kaisa Koskinen ◽  
Maximilian Mora ◽  
Michael Beck ◽  
Lisa Wink ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Human Health ◽  
Gene Targeting ◽  
Gut Microbiome ◽  
Rrna Gene ◽  
Stool Samples ◽  
Human Stool

AbstractThe gut microbiome is strongly interwoven with human health. Conventional gut microbiome analysis generally involves 16S rRNA gene targeting next generation sequencing (NGS) of stool microbial communities, and correlation of results with clinical parameters. However, some microorganisms may not be alive at the time of sampling, and thus their impact on the human health is potentially less significant. As conventional NGS methods do not differentiate between viable and dead microbial components, retrieved results provide only limited information.Propidium monoazide (PMA) is frequently used in food safety monitoring and other disciplines to discriminate living from dead cells. PMA binds to free DNA and masks it for subsequent procedures. In this article we show the impact of PMA on the results of 16S rRNA gene-targeting NGS from human stool samples and validate the optimal applicable concentration to achieve a reliable detection of the living microbial communities.Fresh stool samples were treated with a concentration series of zero to 300 μM PMA, and were subsequently subjected to amplicon-based NGS. The results indicate that a substantial proportion of the human microbial community is not intact at the time of sampling. PMA treatment significantly reduced the diversity and richness of the sample depending on the concentration and impacted the relative abundance of certain important microorganisms (e.g. Akkermansia, Bacteroides). Overall, we found that a concentration of 100 μM PMA was sufficient to quench signals from disrupted microbial cells.The optimized protocol proposed here can be easily implemented in classical microbiome analyses, and helps to retrieve an improved and less blurry picture of the microbial community composition by excluding signals from background DNA.

scholarly journals Evaluating the Impact of Wastewater Effluent on Microbial Communities in the Panke, an Urban River

Water ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 888 ◽  
Author(s):  
Marcella Nega ◽  
Burga Braun ◽  
Sven Künzel ◽  
Ulrich Szewzyk
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sampling Site ◽  
River Sediments ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Alpha And Beta Diversity ◽  
The Impact

Pharmaceuticals are consumed in high amounts and can enter as emerging organic compounds in surface waters as they are only partially retained in wastewater treatment plants (WWTPs). Receiving pharmaceuticals may burden the aquatic environment, as they are designed to be bioactive even at low concentrations. Sediment biofilm populations were analyzed in river sediments due to the exposure of an inflow of WWTP effluents. Illumina MiSeq 16S rRNA gene amplicon sequencing was performed of 108 sediment samples, which were taken from multiple cores within three sampling locations in the Panke River, with one sampling site located downstream of the inflow. Sequencing data were processed to infer microbial community structure in samples concerning the environmental variables, such as micropollutants and physicochemical parameters measured for each core. More than 25 different micropollutants were measured in pore water samples, in which bezafibrate, clofibric acid, carbamazepine, and diclofenac were detected at high concentrations. Bacterial 16S rRNA gene amplicons revealed Nitrospirae, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Bacteroidetes, and Ignavibacteriae as the most abundant groups in the samples. Differences in microbial community composition were observed with respect to micropollutants. However, our findings revealed that the composition of the microbial community was not only governed by the effluent. The significant changes in the alpha- and beta-diversity were explained by phenobarbital and SO42−, which did not originate from the WWTP indicating that more unobserved factors are also likely to play a role in affecting the biofilm community’s composition.

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