scholarly journals Microbial Community Response during the Iron Fertilization Experiment LOHAFEX

2012 ◽  
Vol 78 (24) ◽  
pp. 8803-8812 ◽  
Author(s):  
Stefan Thiele ◽  
Bernhard M. Fuchs ◽  
Nagappa Ramaiah ◽  
Rudolf Amann
Keyword(s):  
Microbial Community ◽  
Total Cell ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Thymidine Uptake ◽  
Phytoplankton Blooms ◽  
Minor Response ◽  
Content Type ◽  
Cell Numbers ◽  
Iron Fertilization

ABSTRACTIron fertilization experiments in high-nutrient, low-chlorophyll areas are known to induce phytoplankton blooms. However, little is known about the response of the microbial community upon iron fertilization. As part of the LOHAFEX experiment in the southern Atlantic Ocean,BacteriaandArchaeawere monitored within and outside an induced bloom, dominated byPhaeocystis-like nanoplankton, during the 38 days of the experiment. The microbial production increased 1.6-fold (thymidine uptake) and 2.1-fold (leucine uptake), while total cell numbers increased only slightly over the course of the experiment. 454 tag pyrosequencing of partial 16S rRNA genes and catalyzed reporter deposition fluorescencein situhybridization (CARD FISH) showed that the composition and abundance of the bacterial and archaeal community in the iron-fertilized water body were remarkably constant without development of typical bloom-related succession patterns. Members of groups usually found in phytoplankton blooms, such asRoseobacterandGammaproteobacteria, showed no response or only a minor response to the bloom. However, sequence numbers and total cell numbers of the SAR11 and SAR86 clades increased slightly but significantly toward the end of the experiment. It seems that although microbial productivity was enhanced within the fertilized area, a succession-like response of the microbial community upon the algal bloom was averted by highly effective grazing. Only small-celled members like the SAR11 and SAR86 clades could possibly escape the grazing pressure, explaining a net increase of those clades in numbers.

scholarly journals Defining the Core Citrus Leaf- and Root-Associated Microbiota: Factors Associated with Community Structure and Implications for Managing Huanglongbing (Citrus Greening) Disease

2017 ◽  
Vol 83 (11) ◽  
Author(s):  
Ryan A. Blaustein ◽  
Graciela L. Lorca ◽  
Julie L. Meyer ◽  
Claudio F. Gonzalez ◽  
Max Teplitski
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Sequencing ◽  
Symptom Severity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
The Core ◽  
Symptom Progression

ABSTRACTStable associations between plants and microbes are critical to promoting host health and productivity. The objective of this work was to test the hypothesis that restructuring of the core microbiota may be associated with the progression of huanglongbing (HLB), the devastating citrus disease caused byLiberibacter asiaticus,Liberibacter americanus, andLiberibacter africanus. The microbial communities of leaves (n= 94) and roots (n= 79) from citrus trees that varied by HLB symptom severity, cultivar, location, and season/time were characterized with Illumina sequencing of 16S rRNA genes. The taxonomically rich communities contained abundant core members (i.e., detected in at least 95% of the respective leaf or root samples), some overrepresented site-specific members, and a diverse community of low-abundance variable taxa. The composition and diversity of the leaf and root microbiota were strongly associated with HLB symptom severity and location; there was also an association with host cultivar. The relative abundance ofLiberibacterspp. among leaf microbiota positively correlated with HLB symptom severity and negatively correlated with alpha diversity, suggesting that community diversity decreases as symptoms progress. Network analysis of the microbial community time series identified a mutually exclusive relationship betweenLiberibacterspp. and members of theBurkholderiaceae,Micromonosporaceae, andXanthomonadaceae. This work confirmed several previously described plant disease-associated bacteria, as well as identified new potential implications for biological control. Our findings advance the understanding of (i) plant microbiota selection across multiple variables and (ii) changes in (core) community structure that may be a precondition to disease establishment and/or may be associated with symptom progression.IMPORTANCEThis study provides a comprehensive overview of the core microbial community within the microbiomes of plant hosts that vary in extent of disease symptom progression. With 16S Illumina sequencing analyses, we not only confirmed previously described bacterial associations with plant health (e.g., potentially beneficial bacteria) but also identified new associations and potential interactions between certain bacteria and an economically important phytopathogen. The importance of core taxa within broader plant-associated microbial communities is discussed.

scholarly journals Simple Absolute Quantification Method Correcting for Quantitative PCR Efficiency Variations for Microbial Community Samples

2012 ◽  
Vol 78 (12) ◽  
pp. 4481-4489 ◽  
Author(s):  
Robert Brankatschk ◽  
Natacha Bodenhausen ◽  
Josef Zeyer ◽  
Helmut Bürgmann
Keyword(s):  
Microbial Community ◽  
Quantitative Pcr ◽  
Environmental Samples ◽  
Absolute Quantification ◽  
Geobacter Sulfurreducens ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gene Copy ◽  
Nostoc Commune ◽  
Content Type

ABSTRACTReal-time quantitative PCR (qPCR) is a widely used technique in microbial community analysis, allowing the quantification of the number of target genes in a community sample. Currently, the standard-curve (SC) method of absolute quantification is widely employed for these kinds of analysis. However, the SC method assumes that the amplification efficiency (E) is the same for both the standard and the sample target template. We analyzed 19 bacterial strains and nine environmental samples in qPCR assays, targeting thenifHand 16S rRNA genes. TheEvalues of the qPCRs differed significantly, depending on the template. This has major implications for the quantification. If the sample and standard differ in theirEvalues, quantification errors of up to orders of magnitude are possible. To address this problem, we propose and test the one-point calibration (OPC) method for absolute quantification. The OPC method corrects for differences inEand was derived from the ΔΔCTmethod with correction forE, which is commonly used for relative quantification in gene expression studies. The SC and OPC methods were compared by quantifying artificial template mixtures fromGeobacter sulfurreducens(DSM 12127) andNostoc commune(Culture Collection of Algae and Protozoa [CCAP] 1453/33), which differ in theirEvalues. While the SC method deviated from the expectednifHgene copy number by 3- to 5-fold, the OPC method quantified the template mixtures with high accuracy. Moreover, analyzing environmental samples, we show that even small differences inEbetween the standard and the sample can cause significant differences between the copy numbers calculated by the SC and the OPC methods.

scholarly journals Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems

2015 ◽  
Vol 81 (13) ◽  
pp. 4246-4252 ◽  
Author(s):  
Yan Yan ◽  
Eiko E. Kuramae ◽  
Peter G. L. Klinkhamer ◽  
Johannes A. van Veen
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Terrestrial Ecosystems ◽  
Diversity Indices ◽  
Soil Samples ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Dilution Method ◽  
Soil Suspension ◽  
Content Type

ABSTRACTIt is hard to assess experimentally the importance of microbial diversity in soil for the functioning of terrestrial ecosystems. An approach that is often used to make such assessment is the so-called dilution method. This method is based on the assumption that the biodiversity of the microbial community is reduced after dilution of a soil suspension and that the reduced diversity persists after incubation of more or less diluted inocula in soil. However, little is known about how the communities develop in soil after inoculation. In this study, serial dilutions of a soil suspension were made and reinoculated into the original soil previously sterilized by gamma irradiation. We determined the structure of the microbial communities in the suspensions and in the inoculated soils using 454-pyrosequencing of 16S rRNA genes. Upon dilution, several diversity indices showed that, indeed, the diversity of the bacterial communities in the suspensions decreased dramatically, withProteobacteriaas the dominant phylum of bacteria detected in all dilutions. The structure of the microbial community was changed considerably in soil, withProteobacteria,Bacteroidetes, andVerrucomicrobiaas the dominant groups in most diluted samples, indicating the importance of soil-related mechanisms operating in the assembly of the communities. We found unique operational taxonomic units (OTUs) even in the highest dilution in both the suspensions and the incubated soil samples. We conclude that the dilution approach reduces the diversity of microbial communities in soil samples but that it does not allow accurate predictions of the community assemblage during incubation of (diluted) suspensions in soil.

scholarly journals Effect of Sodium Bisulfite Injection on the Microbial Community Composition in a Brackish-Water-Transporting Pipeline

2011 ◽  
Vol 77 (19) ◽  
pp. 6908-6917 ◽  
Author(s):  
Hyung Soo Park ◽  
Indranil Chatterjee ◽  
Xiaoli Dong ◽  
Sheng-Hung Wang ◽  
Christoph W. Sensen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Sodium Bisulfite ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Iron Corrosion ◽  
Injection Point ◽  
Content Type ◽  
Sulfate Reducing

ABSTRACTPipelines transporting brackish subsurface water, used in the production of bitumen by steam-assisted gravity drainage, are subject to frequent corrosion failures despite the addition of the oxygen scavenger sodium bisulfite (SBS). Pyrosequencing of 16S rRNA genes was used to determine the microbial community composition for planktonic samples of transported water and for sessile samples of pipe-associated solids (PAS) scraped from pipeline cutouts representing corrosion failures. These were obtained from upstream (PAS-616P) and downstream (PAS-821TP and PAS-821LP, collected under rapid-flow and stagnant conditions, respectively) of the SBS injection point. Most transported water samples had a large fraction (1.8% to 97% of pyrosequencing reads) ofPseudomonasnot found in sessile pipe samples. The sessile population of PAS-616P had methanogens (Methanobacteriaceae) as the main (56%) community component, whereasDeltaproteobacteriaof the generaDesulfomicrobiumandDesulfocapsawere not detected. In contrast, PAS-821TP and PAS-821LP had lower fractions (41% and 0.6%) ofMethanobacteriaceaearchaea but increased fractions of sulfate-reducingDesulfomicrobium(18% and 48%) and of bisulfite-disproportionatingDesulfocapsa(35% and 22%) bacteria. Hence, SBS injection strongly changed the sessile microbial community populations. X-ray diffraction analysis of pipeline scale indicated that iron carbonate was present both upstream and downstream, whereas iron sulfide and sulfur were found only downstream of the SBS injection point, suggesting a contribution of the bisulfite-disproportionating and sulfate-reducing bacteria in the scale to iron corrosion. Incubation of iron coupons with pipeline waters indicated iron corrosion coupled to the formation of methane. Hence, both methanogenic and sulfidogenic microbial communities contributed to corrosion of pipelines transporting these brackish waters.

scholarly journals Deterministic Assembly of Complex Bacterial Communities in Guts of Germ-Free Cockroaches

2015 ◽  
Vol 82 (4) ◽  
pp. 1256-1263 ◽  
Author(s):  
Aram Mikaelyan ◽  
Claire L. Thompson ◽  
Markus J. Hofer ◽  
Andreas Brune
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Experimental Proof ◽  
Content Type ◽  
Germ Free ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Axenic Conditions

ABSTRACTThe gut microbiota of termites plays important roles in the symbiotic digestion of lignocellulose. However, the factors shaping the microbial community structure remain poorly understood. Because termites cannot be raised under axenic conditions, we established the closely related cockroachShelfordella lateralisas a germ-free model to study microbial community assembly and host-microbe interactions. In this study, we determined the composition of the bacterial assemblages in cockroaches inoculated with the gut microbiota of termites and mice using pyrosequencing analysis of their 16S rRNA genes. Although the composition of the xenobiotic communities was influenced by the lineages present in the foreign inocula, their structure resembled that of conventional cockroaches. Bacterial taxa abundant in conventional cockroaches but rare in the foreign inocula, such asDysgonomonasandParabacteroidesspp., were selectively enriched in the xenobiotic communities. Donor-specific taxa, such as endomicrobia or spirochete lineages restricted to the gut microbiota of termites, however, either were unable to colonize germ-free cockroaches or formed only small populations. The exposure of xenobiotic cockroaches to conventional adults restored their normal microbiota, which indicated that autochthonous lineages outcompete foreign ones. Our results provide experimental proof that the assembly of a complex gut microbiota in insects is deterministic.

scholarly journals Pyrosequencing Analysis of Bacterial Diversity in 14 Wastewater Treatment Systems in China

2012 ◽  
Vol 78 (19) ◽  
pp. 7042-7047 ◽  
Author(s):  
Xiaohui Wang ◽  
Man Hu ◽  
Yu Xia ◽  
Xianghua Wen ◽  
Kun Ding
Keyword(s):  
Wastewater Treatment ◽  
Microbial Community ◽  
Bacterial Community ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Microbial Populations ◽  
Operational Parameters ◽  
Geographic Locations ◽  
Content Type ◽  
Wastewater Treatment Systems

ABSTRACTTo determine if there is a core microbial community in the microbial populations of different wastewater treatment plants (WWTPs) and to investigate the effects of wastewater characteristics, operational parameters, and geographic locations on microbial communities, activated sludge samples were collected from 14 wastewater treatment systems located in 4 cities in China. High-throughput pyrosequencing was used to examine the 16S rRNA genes of bacteria in the wastewater treatment systems. Our results showed that there were 60 genera of bacterial populations commonly shared by all 14 samples, includingFerruginibacter,Prosthecobacter,Zoogloea, Subdivision 3 generaincertae sedis, Gp4, Gp6, etc., indicating that there is a core microbial community in the microbial populations of WWTPs at different geographic locations. The canonical correspondence analysis (CCA) results showed that the bacterial community variance correlated most strongly with water temperature, conductivity, pH, and dissolved oxygen (DO) content. Variance partitioning analyses suggested that wastewater characteristics had the greatest contribution to the bacterial community variance, explaining 25.7% of the variance of bacterial communities independently, followed by operational parameters (23.9%) and geographic location (14.7%). Results of this study provided insights into the bacterial community structure and diversity in geographically distributed WWTPs and discerned the relationships between bacterial community and environmental variables in WWTPs.

scholarly journals Defining the Functional Potential and Active Community Members of a Sediment Microbial Community in a High-Arctic Hypersaline Subzero Spring

2013 ◽  
Vol 79 (12) ◽  
pp. 3637-3648 ◽  
Author(s):  
Chih-Ying Lay ◽  
Nadia C. S. Mykytczuk ◽  
Étienne Yergeau ◽  
Guillaume Lamarche-Gagnon ◽  
Charles W. Greer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Sulfur Metabolism ◽  
Close Association ◽  
High Arctic ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Metagenomic Data ◽  
Metabolic Potential ◽  
Data Set ◽  
Content Type

ABSTRACTThe Lost Hammer (LH) Spring is the coldest and saltiest terrestrial spring discovered to date and is characterized by perennial discharges at subzero temperatures (−5°C), hypersalinity (salinity, 24%), and reducing (≈−165 mV), microoxic, and oligotrophic conditions. It is rich in sulfates (10.0%, wt/wt), dissolved H2S/sulfides (up to 25 ppm), ammonia (≈381 μM), and methane (11.1 g day−1). To determine its total functional and genetic potential and to identify its active microbial components, we performed metagenomic analyses of the LH Spring outlet microbial community and pyrosequencing analyses of the cDNA of its 16S rRNA genes. Reads related toCyanobacteria(19.7%),Bacteroidetes(13.3%), andProteobacteria(6.6%) represented the dominant phyla identified among the classified sequences. Reconstruction of the enzyme pathways responsible for bacterial nitrification/denitrification/ammonification and sulfate reduction appeared nearly complete in the metagenomic data set. In the cDNA profile of the LH Spring active community, ammonia oxidizers (Thaumarchaeota), denitrifiers (Pseudomonasspp.), sulfate reducers (Desulfobulbusspp.), and other sulfur oxidizers (Thermoprotei) were present, highlighting their involvement in nitrogen and sulfur cycling. Stress response genes for adapting to cold, osmotic stress, and oxidative stress were also abundant in the metagenome. Comparison of the composition of the functional community of the LH Spring to metagenomes from other saline/subzero environments revealed a close association between the LH Spring and another Canadian high-Arctic permafrost environment, particularly in genes related to sulfur metabolism and dormancy. Overall, this study provides insights into the metabolic potential and the active microbial populations that exist in this hypersaline cryoenvironment and contributes to our understanding of microbial ecology in extreme environments.

scholarly journals Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Benjamin J. Callahan ◽  
Dmitry Grinevich ◽  
Siddhartha Thakur ◽  
Michael A. Balamotis ◽  
Tuval Ben Yehezkel
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strain Identification ◽  
Long Reads ◽  
Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

scholarly journals Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 865
Author(s):  
Lantian Su ◽  
Xinxin Liu ◽  
Guangyao Jin ◽  
Yue Ma ◽  
Haoxin Tan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Communities ◽  
Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Functional Genes ◽  
Martes Zibellina ◽  
Clear Cutting ◽  
Metabolic Functions

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

scholarly journals Subsoil microbial community responses to air exposure and legume growth depend on soil properties across different depths

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hongmei Yan ◽  
Fan Yang ◽  
Jiamin Gao ◽  
Ziheng Peng ◽  
Weimin Chen
Keyword(s):  
Microbial Community ◽  
Soil Properties ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Profiles ◽  
Air Exposure ◽  
Structure Variation ◽  
Α Diversity ◽  
Different Depths ◽  
Legume Growth

AbstractAnthropogenic disturbance, such as agricultural and architectural activities, can greatly influence belowground soil microbes, and thus soil formation and nutrient cycling. The objective of this study was to investigate microbial community variation in deep soils affected by strong disturbances. In present study, twelve soil samples were collected from different depths (0–300 cm) and placed onto the surface. We investigated the structure variation of the microbial community down through the soil profiles in response to disturbance originated by legume plants (robinia and clover) cultivation vs. plant-free controls. The high-throughput sequencing of 16S rRNA genes showed that microbial α-diversity decreased with depth, and that growing both plants significantly impacted the diversity in the topsoil. The soil profile was clustered into three layers: I (0–40 cm), II (40–120 cm), and III (120–300 cm); with significantly different taxa found among them. Soil properties explained a large amount of the variation (23.5%) in the microbial community, and distinct factors affected microbial assembly in the different layers, e.g., available potassium in layer I, pH and total nitrogen in layer II, pH and organic matter in layer III. The prediction of metabolic functions and oxygen requirements indicated that the number of aerobic bacteria increased with more air exposure, which may further accelerate the transformation of nitrogen, sulfur, carbon, and pesticides in the soil. The diversity of soil microorganisms followed a depth-decay pattern, but became higher following legume growth and air exposure, with notable abundance variation of several important bacterial species, mainly belonging to Nitrospira, Verrucomicrobia, and Planctomycetes, and soil properties occurring across the soil profiles.

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