Seasonal and spatial variations in microbial activity at various phylogenetic resolutions at a groundwater – surface water interface

2014 ◽  
Vol 60 (5) ◽  
pp. 277-286 ◽  
Author(s):  
Ran Yu ◽  
Barth F. Smets ◽  
Ping Gan ◽  
Allison A. MacKay ◽  
Joerg Graf
Keyword(s):  
Surface Water ◽  
16S Rrna ◽  
Microbial Activity ◽  
Clone Library ◽  
Iron Oxidation ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Water Interface ◽  
Microbial Activities ◽  
Microbial Iron Oxidation

We investigated the seasonal and spatial variation in activity and density of the metabolically active in situ microbial community (AIMC) at a landfill leachate-impacted groundwater – surface water interface (GSI). A series of AIMC traps were designed and implemented for AIMC sampling and microbial activity and density examinations. Measurements were made not only at the level of bacterial domain but also at the levels of alphaproteobacterial Rhizobiales order and gammaproteobacterial Pseudomonas genus, both of which included a large number of iron-oxidizing bacteria as revealed from previous analysis. Consistently higher microbial activities with less variation in depth were measured in the AIMC traps than in the ambient sediments. Flood disturbance appeared to control AIMC activity distributions at the gradually elevated GSI. The highest AIMC activities were generally obtained from locations closest to the free surface water boundary except during the dry season when microbial activities were similar across the entire GSI. A clone library of AIMC 16S rRNA genes was constructed, and it confirmed the predominant role of the targeted alphaproteobacterial group in AIMC activity and composition. This taxon constituted 2%–14% of all bacteria with similar activity distribution profiles. The Pseudomonas group occupied only 0.1‰–0.5‰ of the total bacterial density, but its activity was 27 times higher than the bacterial average. Of the 16S rRNA sequences in the AIMC clone library, 7.5% were phylogenetically related to putative IOB, supporting the occurrence and persistence of active microbial iron oxidation across the studied iron-rich GSI ecosystem.

scholarly journals Assessment of the Diversity, Abundance, and Ecological Distribution of Members of Candidate Division SR1 Reveals a High Level of Phylogenetic Diversity but Limited Morphotypic Diversity

2009 ◽  
Vol 75 (12) ◽  
pp. 4139-4148 ◽  
Author(s):  
James P. Davis ◽  
Noha H. Youssef ◽  
Mostafa S. Elshahed
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Clone Library ◽  
Phylogenetic Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Qpcr Analysis ◽  
Freshwater Pond ◽  
Candidate Division

ABSTRACT We used a combination of 16S rRNA gene clone library surveys, quantitative PCR (qPCR) analysis, and fluorescent in situ hybridization to investigate the diversity, abundance, and distribution of members of candidate division SR1 in multiple habitats. Using SR1-specific 16S rRNA gene primers, we identified multiple novel SR1 lineages in four different anaerobic environments: sediments from Zodletone Spring, a sulfide- and sulfur-rich spring in southwestern Oklahoma; inner layers of microbial mats obtained from Sperm Pool, a high-temperature, low-pH pool (55°C, pH 2.5) in Yellowstone National Park; fresh bovine ruminal contents; and anaerobic freshwater pond sediments (Duck Pond) in Norman, Oklahoma. qPCR analysis indicated that SR1 members constitute a small fraction (<0.01%) of the microbial communities in Duck Pond and ruminal samples but constitute a significant fraction (11.6 and 48.7%) of the total number of bacterial 16S rRNA genes in Zodletone Spring and the inner layers of Sperm Pool microbial mat samples, respectively. By using SR1-specific fluorescent probes, filamentous cells were identified as the sole SR1 morphotype in all environments examined, with the exception of Sperm Pool, where a second bacillus morphotype was also identified. Using a full-cycle 16S rRNA approach, we show that each of these two morphotypes corresponds to a specific phylogenetic lineage identified in the Sperm Pool clone library. This work greatly expands the intralineage phylogenetic diversity within candidate division SR1 and provides valuable quantification and visualization tools that could be used for investigating the ecological roles, dynamics, and genomics of this as-yet-uncultured bacterial phylum.

scholarly journals Microbial Iron Oxidation in the Arctic Tundra and Its Implications for Biogeochemical Cycling

2015 ◽  
Vol 81 (23) ◽  
pp. 8066-8075 ◽  
Author(s):  
David Emerson ◽  
Jarrod J. Scott ◽  
Joshua Benes ◽  
William B. Bowden
Keyword(s):  
Relative Abundance ◽  
Iron Oxidation ◽  
Arctic Tundra ◽  
16S Rrna Genes ◽  
The Arctic ◽  
Rrna Genes ◽  
Oxygenic Photosynthesis ◽  
Field Station ◽  
Content Type ◽  
Microbial Iron Oxidation

ABSTRACTThe role that neutrophilic iron-oxidizing bacteria play in the Arctic tundra is unknown. This study surveyed chemosynthetic iron-oxidizing communities at the North Slope of Alaska near Toolik Field Station (TFS) at Toolik Lake (lat 68.63, long −149.60). Microbial iron mats were common in submerged habitats with stationary or slowly flowing water, and their greatest areal extent is in coating plant stems and sediments in wet sedge meadows. Some Fe-oxidizing bacteria (FeOB) produce easily recognized sheath or stalk morphotypes that were present and dominant in all the mats we observed. The cool water temperatures (9 to 11°C) and reduced pH (5.0 to 6.6) at all sites kinetically favor microbial iron oxidation. A microbial survey of five sites based on 16S rRNA genes found a predominance ofProteobacteria, withBetaproteobacteriaand members of the familyComamonadaceaebeing the most prevalent operational taxonomic units (OTUs). In relative abundance, clades of lithotrophic FeOB composed 5 to 10% of the communities. OTUs related to cyanobacteria and chloroplasts accounted for 3 to 25% of the communities. Oxygen profiles showed evidence for oxygenic photosynthesis at the surface of some mats, indicating the coexistence of photosynthetic and FeOB populations. The relative abundance of OTUs belonging to putative Fe-reducing bacteria (FeRB) averaged around 11% in the sampled iron mats. Mats incubated anaerobically with 10 mM acetate rapidly initiated Fe reduction, indicating that active iron cycling is likely. The prevalence of iron mats on the tundra might impact the carbon cycle through lithoautotrophic chemosynthesis, anaerobic respiration of organic carbon coupled to iron reduction, and the suppression of methanogenesis, and it potentially influences phosphorus dynamics through the adsorption of phosphorus to iron oxides.

scholarly journals Phylogeny of Microorganisms Populating a Thick, Subaerial, Predominantly Lithotrophic Biofilm at an Extreme Acid Mine Drainage Site

2000 ◽  
Vol 66 (9) ◽  
pp. 3842-3849 ◽  
Author(s):  
Philip L. Bond ◽  
Steven P. Smriga ◽  
Jillian F. Banfield
Keyword(s):  
Acid Mine Drainage ◽  
16S Rrna ◽  
New Genus ◽  
Mine Drainage ◽  
Iron Oxidation ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Metal Reduction ◽  
Acid Mine ◽  
Metabolic Feature

ABSTRACT An unusually thick (∼1 cm) slime developed on a slump of finely disseminated pyrite ore within an extreme acid mine drainage site at Iron Mountain, near Redding, Calif. The slime was studied over the period of 1 year. The subaerial form of the slime distinguished it from more typical submerged streamers. Phylogenetic analysis of 16S rRNA genes revealed a diversity of sequences that were mostly novel. Nearest relatives to the majority of sequences came from iron-oxidizing acidophiles, and it appears that iron oxidation is the predominant metabolic characteristic of the organisms in the slime. The most abundant of the 16S rRNA genes detected were from organisms related toLeptospirillum species. The dominant sequence (71% of clones) may represent a new genus. Sequences within theArchaea of the Thermoplasmales lineage were detected. Most of these were only distantly related to known microorganisms. Also, sequences affiliating withAcidimicrobium were detected. Some of these were closely related to “Ferromicrobium acidophilus,” and others were affiliated with a lineage only represented by environmental clones. Unexpectedly, sequences that affiliated within the delta subdivision of the Proteobacteria were detected. The predominant metabolic feature of bacteria of this subdivision is anaerobic sulfate or metal reduction. Thus, microenvironments of low redox potential possibly exist in the predominantly oxidizing environments of the slime. These results expand our knowledge of the biodiversity of acid mine drainage environments and extend our understanding of the ecology of extremely acidic systems.

scholarly journals Selective Phylogenetic Analysis Targeted at 16S rRNA Genes of Thermophiles and Hyperthermophiles in Deep-Subsurface Geothermal Environments

2006 ◽  
Vol 72 (1) ◽  
pp. 21-27 ◽  
Author(s):  
Hiroyuki Kimura ◽  
Maki Sugihara ◽  
Kenji Kato ◽  
Satoshi Hanada
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
River Water ◽  
Clone Library ◽  
Hot Spring ◽  
Drilling Fluid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Deep Subsurface

ABSTRACT Deep-subsurface samples obtained by deep drilling are likely to be contaminated with mesophilic microorganisms in the drilling fluid, and this could affect determination of the community structure of the geothermal microflora using 16S rRNA gene clone library analysis. To eliminate possible contamination by PCR-amplified 16S rRNA genes from mesophiles, a combined thermal denaturation and enzyme digestion method, based on a strong correlation between the G+C content of the 16S rRNA gene and the optimum growth temperatures of most known prokaryotic cultures, was used prior to clone library construction. To validate this technique, hot spring fluid (76°C) and river water (14°C) were used to mimic a deep-subsurface sample contaminated with drilling fluid. After DNA extraction and PCR amplification of the 16S rRNA genes from individual samples separately, the amplified products from river water were observed to be denatured at 82°C and completely digested by exonuclease I (Exo I), while the amplified products from hot spring fluid remained intact after denaturation at 84°C and enzyme digestion with Exo I. DNAs extracted from the two samples were mixed and used as a template for amplification of the 16S rRNA genes. The amplified rRNA genes were denatured at 84°C and digested with Exo I before clone library construction. The results indicated that the 16S rRNA gene sequences from the river water were almost completely eliminated, whereas those from the hot spring fluid remained.

scholarly journals Characterization of the Prokaryotic Diversity in Cold Saline Perennial Springs of the Canadian High Arctic

2007 ◽  
Vol 73 (5) ◽  
pp. 1532-1543 ◽  
Author(s):  
Nancy N. Perreault ◽  
Dale T. Andersen ◽  
Wayne H. Pollard ◽  
Charles W. Greer ◽  
Lyle G. Whyte
Keyword(s):  
16S Rrna ◽  
Clone Library ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Geographic Origin ◽  
High Arctic ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Cold Environments ◽  
Gradient Gel Electrophoresis ◽  
High Concentrations

ABSTRACT The springs at Gypsum Hill and Colour Peak on Axel Heiberg Island in the Canadian Arctic originate from deep salt aquifers and are among the few known examples of cold springs in thick permafrost on Earth. The springs discharge cold anoxic brines (7.5 to 15.8% salts), with a mean oxidoreduction potential of −325 mV, and contain high concentrations of sulfate and sulfide. We surveyed the microbial diversity in the sediments of seven springs by denaturing gradient gel electrophoresis (DGGE) and analyzing clone libraries of 16S rRNA genes amplified with Bacteria and Archaea-specific primers. Dendrogram analysis of the DGGE banding patterns divided the springs into two clusters based on their geographic origin. Bacterial 16S rRNA clone sequences from the Gypsum Hill library (spring GH-4) were classified into seven phyla (Actinobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes, Proteobacteria, Spirochaetes, and Verrucomicrobia); Deltaproteobacteria and Gammaproteobacteria sequences represented half of the clone library. Sequences related to Proteobacteria (82%), Firmicutes (9%), and Bacteroidetes (6%) constituted 97% of the bacterial clone library from Colour Peak (spring CP-1). Most GH-4 archaeal clone sequences (79%) were related to the Crenarchaeota while half of the CP-1 sequences were related to orders Halobacteriales and Methanosarcinales of the Euryarchaeota. Sequences related to the sulfur-oxidizing bacterium Thiomicrospira psychrophila dominated both the GH-4 (19%) and CP-1 (45%) bacterial libraries, and 56 to 76% of the bacterial sequences were from potential sulfur-metabolizing bacteria. These results suggest that the utilization and cycling of sulfur compounds may play a major role in the energy production and maintenance of microbial communities in these unique, cold environments.

scholarly journals Molecular Evidence for an Active Microbial Methane Cycle in Subsurface Serpentinite-Hosted Groundwaters in the Samail Ophiolite, Oman

2020 ◽  
Vol 87 (2) ◽  
Author(s):  
Emily A. Kraus ◽  
Daniel Nothaft ◽  
Blake W. Stamps ◽  
Kaitlin R. Rempfert ◽  
Eric T. Ellison ◽  
...  
Keyword(s):  
Low Temperature ◽  
16S Rrna ◽  
Microbial Activity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Molecular Evidence ◽  
Metagenomic Sequencing ◽  
Production Of Hydrogen ◽  
Genes Encoding ◽  
Subsurface Waters

ABSTRACT Serpentinization can generate highly reduced fluids replete with hydrogen (H2) and methane (CH4), potent reductants capable of driving microbial methanogenesis and methanotrophy, respectively. However, CH4 in serpentinized waters is thought to be primarily abiogenic, raising key questions about the relative importance of methanogens and methanotrophs in the production and consumption of CH4 in these systems. Herein, we apply molecular approaches to examine the functional capability and activity of microbial CH4 cycling in serpentinization-impacted subsurface waters intersecting multiple rock and water types within the Samail Ophiolite of Oman. Abundant 16S rRNA genes and transcripts affiliated with the methanogenic genus Methanobacterium were recovered from the most alkaline (pH, >10), H2- and CH4-rich subsurface waters. Additionally, 16S rRNA genes and transcripts associated with the aerobic methanotrophic genus Methylococcus were detected in wells that spanned varied fluid geochemistry. Metagenomic sequencing yielded genes encoding homologs of proteins involved in the hydrogenotrophic pathway of microbial CH4 production and in microbial CH4 oxidation. Transcripts of several key genes encoding methanogenesis/methanotrophy enzymes were identified, predominantly in communities from the most hyperalkaline waters. These results indicate active methanogenic and methanotrophic populations in waters with hyperalkaline pH in the Samail Ophiolite, thereby supporting a role for biological CH4 cycling in aquifers that undergo low-temperature serpentinization. IMPORTANCE Serpentinization of ultramafic rock can generate conditions favorable for microbial methane (CH4) cycling, including the abiotic production of hydrogen (H2) and possibly CH4. Systems of low-temperature serpentinization are geobiological targets due to their potential to harbor microbial life and ubiquity throughout Earth’s history. Biomass in fracture waters collected from the Samail Ophiolite of Oman, a system undergoing modern serpentinization, yielded DNA and RNA signatures indicative of active microbial methanogenesis and methanotrophy. Intriguingly, transcripts for proteins involved in methanogenesis were most abundant in the most highly reacted waters that have hyperalkaline pH and elevated concentrations of H2 and CH4. These findings suggest active biological methane cycling in serpentinite-hosted aquifers, even under extreme conditions of high pH and carbon limitation. These observations underscore the potential for microbial activity to influence the isotopic composition of CH4 in these systems, which is information that could help in identifying biosignatures of microbial activity on other planets.

scholarly journals Low Intraspecific Diversity in a Polynucleobacter Subcluster Population Numerically Dominating Bacterioplankton of a Freshwater Pond

2005 ◽  
Vol 71 (8) ◽  
pp. 4539-4547 ◽  
Author(s):  
Martin W. Hahn ◽  
Matthias Pöckl ◽  
Qinglong L. Wu
Keyword(s):  
16S Rrna ◽  
Clone Library ◽  
Culture Collection ◽  
Intraspecific Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Bacterial Populations ◽  
Freshwater Pond ◽  
Phylogenetic Resolution

ABSTRACT Cultivation-dependent and -independent methods were combined to investigate the microdiversity of a Polynucleobacter subcluster population (Betaproteobacteria) numerically dominating the bacterioplankton of a small, humic freshwater pond. Complete coverage of the population by cultivation allowed the analysis of microdiversity beyond the phylogenetic resolution of ribosomal markers. Fluorescent in situ hybridization with two probes specific for the narrow subcluster C (PnecC bacteria) of the Polynucleobacter cluster revealed that this population contributed up to 60% to the total number of bacterioplankton cells. Microdiversity was investigated for a date at which the highest relative numbers of PnecC were observed. A clone library of fragments of the ribosomal operon (16S rRNA genes, complete 16S-23S internal transcribed spacer 1 [ITS1], partial 23S rRNA genes) amplified with universal bacterial primers was constructed. The library was stepwise screened for fragments from PnecC bacteria and for different ITS genotypes of PnecC bacteria. The isolated PnecC strains were characterized by sequencing of the 16S rRNA genes and the ITS1. Both the clone library and the established culture collection contained only the same three ITS genotypes, and one of them contributed 46% to the entire number of clones. Genomic fingerprinting of the isolates with several methods always resulted in the detection of only one fingerprint per ITS genotype. We conclude that a Polynucleobacter population with an extremely low intraspecific diversity and an uneven structure numerically dominated the bacterioplankton community in the investigated habitat. This low intraspecific diversity is in strong contrast to the high intraspecific diversities found in marine bacterial populations.

Acidianus Brierleyi is the Dominant Thermoacidophile in a Bioleaching Community Processing Chalcopyrite Containing Concentrates at 70°C

2009 ◽  
Vol 71-73 ◽  
pp. 67-70 ◽  
Author(s):  
Inez J.T. Dinkla ◽  
Mariekie Gericke ◽  
B.K. Geurkink ◽  
Kevin B. Hallberg
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Clone Library ◽  
Rflp Analysis ◽  
16S Rrna Genes ◽  
Qualitative Assessment ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Multi Stage ◽  
Acidianus Brierleyi

Bioleaching test work was performed in continuously operated multi-stage reactor systems at 70°C using a thermophilic culture treating an Aguablanca Ni-Cu concentrate from Spain and a blend of Cu concentrates from Bor, Serbia. The copper in both these concentrates occurs as chalcopyrite and therefore the use of thermophiles was applied, which resulted in copper recoveries of over 95%. Qualitative assessment of the microbial community in the bioreactors was performed by terminal restriction enzyme fragment length polymorphism (T-RFLP) and clone library analysis of the 16S rRNA genes amplified by PCR. T-RFLP analysis revealed that only archaea were present, and that the communities in both the Aguablanca and Bor systems consisted of two different microorganisms. A 16S rRNA gene clone library using DNA from the Aguablanca system was constructed and screened. Again, two archaea were detected in similar relative abundance in the population as found by T-RFLP analyses. The sequences of these two cloned genes revealed that the dominant archaeon (up to 98% of the total archaea detected) was Acidianus brierleyi, and the other was Metallosphaera sedula. Quantitative assessment of the microbial community was performed by Q-PCR and confirmed the dominance of archaea in the system with Acidianus being the dominant strain (98-99% of the total population) and a minor part of the population (1-2%) consisted of Metallosphaera. Additionally, very small amounts of Sulfolobus spp. were detected. This study, along with other recent studies on the diversity of thermoacidophiles involved in the solubilization of copper from chalcopyrite concentrates, revealed that a wider variety of thermoacidophiles are involved in bioprocessing of metal sulfides, and showed that A. brierleyi should be considered an important biomining acidophile.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

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