scholarly journals Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor

2013 ◽  
Vol 79 (24) ◽  
pp. 7790-7799 ◽  
Author(s):  
Karen G. Lloyd ◽  
Megan K. May ◽  
Richard T. Kevorkian ◽  
Andrew D. Steen
Keyword(s):  
Marine Sediments ◽  
Best Practice ◽  
Meta Analysis ◽  
Proteinase K ◽  
Taqman Probe ◽  
Rrna Gene ◽  
Cell Counts ◽  
Catalyzed Reporter Deposition ◽  
High Yields ◽  
Card Fish

ABSTRACTThere is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescentin situhybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined “yield” to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly.

scholarly journals A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy)

2020 ◽  
Vol 8 (6) ◽  
pp. 936 ◽  
Author(s):  
Claudia Leoni ◽  
Mariateresa Volpicella ◽  
Bruno Fosso ◽  
Caterina Manzari ◽  
Elisabetta Piancone ◽  
...  
Keyword(s):  
Ecological Model ◽  
Salinity Range ◽  
Rrna Gene ◽  
Hypervariable Regions ◽  
Cell Counts ◽  
Precious Resource ◽  
Catalyzed Reporter Deposition ◽  
Card Fish ◽  
The 16S Rrna Gene

Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial “Candidatus Aquiluna” (~19% at 14.5% salinity). Interestingly, “Candidatus Aquiluna” had not been identified before in thalassohaline waters.

scholarly journals Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the “Roseobacter Clade” Into a Novel Family, Roseobacteraceae fam. nov.

2021 ◽  
Vol 12 ◽  
Author(s):  
Kevin Y. H. Liang ◽  
Fabini D. Orata ◽  
Yann F. Boucher ◽  
Rebecca J. Case
Keyword(s):  
Best Practice ◽  
Sequence Similarity ◽  
Meta Analysis ◽  
Rrna Gene ◽  
Whole Genome ◽  
Roseobacter Clade ◽  
Phenotypic Data ◽  
New Family ◽  
The Family ◽  
Type Strains

The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, and phylogenetic characteristics, was not always followed. Early efforts for classification relied heavily on 16S rRNA gene sequence similarity and resulted in numerous taxonomic inconsistencies, with several poly- and paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained for most type strains, making a revision of their taxonomy possible. In this study, we performed whole-genome phylogenetic and genotypic analyses combined with a meta-analysis of phenotypic data to review taxonomic classifications of 331 type strains (under 119 genera) within the Rhodobacteraceae family. Representatives of the roseobacter clade not only have different environmental adaptions from other Rhodobacteraceae isolates but were also found to be distinct based on genomic, phylogenetic, and in silico-predicted phenotypic data. As such, we propose to move this group of bacteria into a new family, Roseobacteraceae fam. nov. In total, reclassifications resulted to 327 species and 128 genera, suggesting that misidentification is more problematic at the genus than species level. By resolving taxonomic inconsistencies of type strains within this family, we have established a set of coherent criteria based on whole-genome-based analyses that will help guide future taxonomic efforts and prevent the propagation of errors.

scholarly journals Combining Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization and Microautoradiography To Detect Substrate Utilization by Bacteria and Archaea in the Deep Ocean

2004 ◽  
Vol 70 (7) ◽  
pp. 4411-4414 ◽  
Author(s):  
Eva Teira ◽  
Thomas Reinthaler ◽  
Annelie Pernthaler ◽  
Jakob Pernthaler ◽  
Gerhard J. Herndl
Keyword(s):  
North Atlantic ◽  
Deep Ocean ◽  
Proteinase K ◽  
Detection Rates ◽  
The North ◽  
Deep Waters ◽  
The North Atlantic ◽  
Catalyzed Reporter Deposition ◽  
Card Fish

ABSTRACT The recently developed CARD-FISH protocol was refined for the detection of marine Archaea by replacing the lysozyme permeabilization treatment with proteinase K. This modification resulted in about twofold-higher detection rates for Archaea in deep waters. Using this method in combination with microautoradiography, we found that Archaea are more abundant than Bacteria (42% versus 32% of 4′,6′-diamidino-2-phenylindole counts) in the deep waters of the North Atlantic and that a larger fraction of Archaea than of Bacteria takes up l-aspartic acid (19% versus 10%).

scholarly journals Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated hypolimnion of deep freshwater lakes

2016 ◽  
Author(s):  
Yusuke Okazaki ◽  
Shohei Fujinaga ◽  
Atsushi Tanaka ◽  
Ayato Kohzu ◽  
Hideo Oyagi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Water Layer ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Freshwater Lakes ◽  
Ecological Importance ◽  
Rrna Gene Sequencing ◽  
Catalyzed Reporter Deposition ◽  
Card Fish

ABSTRACTFreshwater bacterioplankton in the oxygenated hypolimnion are reportedly dominated by specific members that are distinct from those in the epilimnion. However, no consensus exists regarding the ubiquity and abundance of these bacterioplankton, which is necessary to evaluate their ecological importance. The present study investigated the bacterioplankton community in the oxygenated hypolimnia of 10 deep freshwater lakes. Despite the broad geochemical characteristics of the lakes, 16S rRNA gene sequencing demonstrated that many predominant lineages in the hypolimnion were shared by several lakes and consisted of members occurring in the entire water layer and members specific to the hypolimnion. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) revealed that representative hypolimnion-specific lineages, CL500–11 (Chloroflexi), CL500–3, CL500–37, CL500–15 (Planctomycetes), and the MGI group (Thaumarchaeota), together accounted for 1.5–32.9% of all bacterioplankton in the hypolimnion of the lakes. Furthermore, an analysis of micro-diversification based on single-nucleotide variation in the partial 16S rRNA gene sequence (oligotyping) suggested the presence of hypolimnion-specific ecotypes among the lineages occurring in the entire water layer (e.g., acI and Limnohabitans). Collectively, these results demonstrate the uniqueness, ubiquity, and quantitative significance of bacterioplankton in the oxygenated hypolimnion, motivating future studies to focus on their eco-physiological characteristics.

scholarly journals Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition for the Identification of Marine Bacteria

2002 ◽  
Vol 68 (6) ◽  
pp. 3094-3101 ◽  
Author(s):  
Annelie Pernthaler ◽  
Jakob Pernthaler ◽  
Rudolf Amann
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Heterotrophic Bacteria ◽  
Cell Loss ◽  
Bacterial Cells ◽  
Detection Rates ◽  
Cell Counts ◽  
Catalyzed Reporter Deposition ◽  
Card Fish

ABSTRACT Fluorescence in situ hybridization (FISH) with horseradish peroxidase (HRP)-labeled oligonucleotide probes and tyramide signal amplification, also known as catalyzed reporter deposition (CARD), is currently not generally applicable to heterotrophic bacteria in marine samples. Penetration of the HRP molecule into bacterial cells requires permeabilization procedures that cause high and most probably species-selective cell loss. Here we present an improved protocol for CARD-FISH of marine planktonic and benthic microbial assemblages. After concentration of samples onto membrane filters and subsequent embedding of filters in low-gelling-point agarose, no decrease in bacterial cell numbers was observed during 90 min of lysozyme incubation (10 mg ml−1 at 37°C). The detection rates of coastal North Sea bacterioplankton by CARD-FISH with a general bacterial probe (EUB338-HRP) were significantly higher (mean, 94% of total cell counts; range, 85 to 100%) than that with a monolabeled probe (EUB338-mono; mean, 48%; range, 19 to 66%). Virtually no unspecific staining was observed after CARD-FISH with an antisense EUB338-HRP. Members of the marine SAR86 clade were undetectable by FISH with a monolabeled probe; however, a substantial population was visualized by CARD-FISH (mean, 7%; range, 3 to 13%). Detection rates of EUB338-HRP in Wadden Sea sediments (mean, 81%; range, 53 to 100%) were almost twice as high as the detection rates of EUB338-mono (mean, 44%; range, 25 to 71%). The enhanced fluorescence intensities and signal-to-background ratios make CARD-FISH superior to FISH with directly labeled oligonucleotides for the staining of bacteria with low rRNA content in the marine environment.

scholarly journals Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling

2021 ◽  
Author(s):  
Mathias Flieder ◽  
Joy Buongiorno ◽  
Craig W. Herbold ◽  
Bela Hausmann ◽  
Thomas Rattei ◽  
...  
Keyword(s):  
16S Rrna ◽  
Marine Sediments ◽  
Meta Analysis ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Dissimilatory Sulfite Reductase ◽  
Gene Expression Analyses ◽  
Oxygen Nitrous Oxide ◽  
Novel Taxa ◽  
Fjord Sediments

AbstractAcidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, “subdivision 23”) and Ca. Polarisedimenticola (“subdivision 22”), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

Novel Streptomyces sp. reported in 2018: A meta-analysis

2020 ◽  
Vol 18 ◽  
Author(s):  
Sagar Aryal ◽  
Laxmi Neupane ◽  
Rameshwar Adhikari ◽  
Balmukunda Regmi ◽  
Niranjan Koirala ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Meta Analysis ◽  
Antimicrobial Properties ◽  
Data Entry ◽  
Flow Diagram ◽  
Rrna Gene ◽  
Research Papers ◽  
Biosynthesis Gene Cluster ◽  
Streptomyces Species ◽  
Sugar Fermentation

: Streptomyces species are very well known for the production of antimicrobials and enzymes. The objective of this review is to search for the novel Streptomyces isolated in 2018 along with their characteristics and possible antimicrobial properties. The literature search was done according to the PRISMA flow diagram where 28 research papers were eligible for the review. Data entry and analyses were performed using IBM SPSS Statistics version 25 while phylogenetic tree was constructed using Geneious Prime Software. The data on general characteristics, biochemical as well as sugar fermentation tests, 16S rRNA gene sequence similarity and DNA-DNA hybridization relatedness were extracted from the research papers and summarized in tables and figures. The biosynthesis gene cluster (BGC) was identified using ‘antibiotics and secondary metabolite analysis shell-antiSMASH’ which showed the possibility of production of new antibiotics, antifungal and antitumor substances from the 28 novel Streptomyces isolated in 2018 which would contribute to the global effort to fight against growing multidrug-resistance.

scholarly journals Iris-Claw Intraocular Lens: Anterior Chamber or Retropupillary Implantation? A Systematic Review and Meta-Analysis

Medicina ◽  
2021 ◽  
Vol 57 (8) ◽  
pp. 785
Author(s):  
I-Chia Liang ◽  
Yun-Hsiang Chang ◽  
Adrián Hernández Hernández Martínez ◽  
Chi-Feng Hung
Keyword(s):  
Anterior Chamber ◽  
Intraocular Lens ◽  
Meta Analysis ◽  
Secondary Outcome ◽  
Controlled Trials ◽  
Cochrane Central Register ◽  
Randomized Controlled ◽  
Cell Counts ◽  
Iop Elevation ◽  
Iris Claw

Background and Objectives: Iris-claw intraocular lens (ICIOL) could be implanted in the anterior chamber (AC) or retropupillary (RP) in eyes lacking capsular and/or zonular support. Several studies have focused on comparing the efficacy and complications of these two techniques and we designed this research to review the published literatures. Materials and Methods: Peer-reviewed studies were collected through network databases (PubMed, Scopus, Cochrane Central Register of Controlled Trials, and ClinicalTrials.gov) and analyzed. The primary outcome was the standardized mean differences (SMDs) of pre- and post-operative corrected distant visual acuity (CDVA). The secondary outcome was the SMDs of pre- and post-operative intraocular pressure (IOP), endothelial cell counts (ECC), and the odds ratios (ORs) of post-operative IOP elevation and cystoid macular edema (CME). Comprehensive Meta-Analysis software was utilized to conduct statistical analysis. Results: Six studies (one randomized controlled trial and five retrospective case series) were relevant and included a total of 516 eyes (255 and 261 eyes in the AC ICIOL and RP ICIOL groups, respectively). The quantitative analysis showed no significant differences in CDVA (SMD: 0.164, 95% confidence interval (CI): −0.171 to 0.500), ECC (SMD: −0.011, 95% CI: −0.195 to 0.173), and IOP elevation events (OR: 0.797, 95% CI: 0.459 to 1.383). Lesser IOP reduction (SMD: 0.257, 95%CI: 0.023 to 0.490) and a relative increase in the incidence of CME (OR:2.315, 95% CI: 0.950 to 5.637) were observed in the AC ICIOL group compared with RP ICIOL group. Conclusions: Our meta-analysis indicated that AC and RP ICIOL seem to have equivalent visual outcomes. RP ICIOL may perform slightly better with more IOP reduction and lesser CME. More randomized controlled trials, which have higher patient participation and more outcomes are needed to confirm our conclusions.

A Test-Retest Reliability Generalization Meta-Analysis of Judgments Via the Policy-Capturing Technique

2021 ◽  
pp. 109442812110115
Author(s):  
Ze Zhu ◽  
Alan J. Tomassetti ◽  
Reeshad S. Dalal ◽  
Shannon W. Schrader ◽  
Kevin Loo ◽  
...  
Keyword(s):  
Best Practice ◽  
Meta Analysis ◽  
Temporal Stability ◽  
Future Research ◽  
Policy Capturing ◽  
Reliability Estimate ◽  
Reliability Generalization ◽  
Retest Reliability ◽  
Reliability Estimates ◽  
Test Retest Reliability

Policy capturing is a widely used technique, but the temporal stability of policy-capturing judgments has long been a cause for concern. This article emphasizes the importance of reporting reliability, and in particular test-retest reliability, estimates in policy-capturing studies. We found that only 164 of 955 policy-capturing studies (i.e., 17.17%) reported a test-retest reliability estimate. We then conducted a reliability generalization meta-analysis on policy-capturing studies that did report test-retest reliability estimates—and we obtained an average reliability estimate of .78. We additionally examined 16 potential methodological and substantive antecedents to test-retest reliability (equivalent to moderators in validity generalization studies). We found that test-retest reliability was robust to variation in 14 of the 16 factors examined but that reliability was higher in paper-and-pencil studies than in web-based studies and was higher for behavioral intention judgments than for other (e.g., attitudinal and perceptual) judgments. We provide an agenda for future research. Finally, we provide several best-practice recommendations for researchers (and journal reviewers) with regard to (a) reporting test-retest reliability, (b) designing policy-capturing studies for appropriate reportage, and (c) properly interpreting test-retest reliability in policy-capturing studies.

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