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 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 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 Comparison of the effects of three fungicides on clubroot disease of tumorous stem mustard and soil bacterial community

2021 ◽  
Author(s):  
Jingjing Liao ◽  
Luyun Luo ◽  
Li Zhang ◽  
Lingzhi Wang ◽  
Xuedan Shi ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Soil Properties ◽  
Soil Microbial Community ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Post Inoculation ◽  
Clubroot Disease ◽  
Soil Microbial ◽  
Α Diversity

Abstract Purpose The application of fungicides is one of the main strategies to prevent clubroot disease. Currently, numerous studies focus on changes in the soil microbial community at different levels of clubroot disease severity. However, the effects of fungicides on the soil microbial community and causative pathogen, Plasmodiophora brassicae, while preventing clubroot disease remain unclear. Methods In this study, we evaluated the control efficacy of three fungicides (fluazinam, metalaxyl-mancozeb, and carbendazim) on clubroot disease of tumorous stem mustard in greenhouse experiment. Uninoculated and Water treatments after inoculation were performed as controls. At three (3 W) and six weeks (6 W) post-inoculation of P. brassicae, soil properties, bacterial composition (sequencing of 16S rRNA genes), and effector gene expression of the pathogen were analyzed. The correlation of these factors with disease index (DI) was explored. Results Fluazinam was the most effective in controlling clubroot disease of tumorous stem mustard with a controlled efficacy of 59.81%, and the abundance of P. brassicae in the soil decreased 21.29% after 3 weeks of treatment. Compared with other treatments, twelve out of twenty effector genes showed higher expression in fluazinam 3 W samples. Different fungicides had different effects on soil properties. EC (electrical conductivity), the main factor that positively associated with DI, was significantly lower in fluazinam treatment than the other two fungicide treatments. The application of fungicides, especially carbendazim, significantly reduced bacterial α-diversity and the composition of soil bacteria. Pseudomonas, Microbacterium, and Sphingobacterium (positively correlated with DI) were enriched in Water, metalaxyl-mancozeb, and carbendazim treatments, but were less abundant in fluazinam treatment. Among the three fungicide treatments, DI was significantly negatively correlated with Shannon and Chao 1 indices. Soil properties and the top bacterial genera that positively correlated with DI were influenced to a lesser degree in the fluazinam treatment. Conclusion Among three fungicides, fluazinam was the most effective agent with the highest control effects against clubroot disease. The strong virulence of fluazinam against P. brassicae was one of the main reasons for the prevention of clubroot disease, and in addition the alteration of rhizosphere bacterial community by fluazinam to the detriment of P. brassicae infection. Based on our results, EC could be an indicator of the severity of clubroot disease.

scholarly journals The relationship between benthic nutrient fluxes and bacterial community in Aquaculture tail-water treatment systems

2021 ◽  
Author(s):  
Regan Nicholaus ◽  
Betina Lukwambe ◽  
Wen Yang ◽  
Zhongming Zheng
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
16S Rrna ◽  
Constructed Wetland ◽  
High Throughput Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nutrient Fluxes ◽  
Benthic Nutrient Fluxes ◽  
Tail Water

Constructed-wetlands, Biofilms, and sedimentation are potential aquaculture tail-water treatments however their roles on the distribution of benthic microbial community and the way they affect the interaction between microbial community and inorganic nutrient fluxes have not been fully explored. This study applied 16S rRNA high-throughput sequencing technology to investigate the microbial community distribution and their link with nutrient fluxes in an aquaculture tail- water bioremediation system . Results showed that bacterial community compositions were significantly different in constructed-wetland and biofilm treatments (p<0.05) relative to sedimentation. The composition of the 16S rRNA genes among all the treatments was enriched with Proteobacteria, Bacteroidetes, Firmicutes, and Flavobacteria . NMDS analysis showed that the bacterial composition in constructed-wetland and biofilm samples clustered separately compared to those in sedimentation. The Functional-Annotation-of-Prokaryotic-Taxa analysis indicated that the proportions of sediment-microbial-functional groups (aerobic-chemoheterophy, chemoheterotrophy, and nitrate-ammonification combined) in the constructed-wetland treatment were 47%, 32% in biofilm and 13% in sedimentation system. Benthic-nutrient fluxes for phosphate, ammonium, nitrite, nitrate and sediment oxygen consumption differed markedly among the treatments ( p<0.05 ). Canonical correspondence analysis indicated constructed-wetland had the strongest association between biogeochemical contents and the bacterial community relative to other treatments. This study suggests that the microbial community distributions and their interactions nutrient fluxes were most improved in the constructed-wetland followed by the area under biofilm and sedimentation treatment.

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 Permeable Reactive Barriers Designed To Mitigate Eutrophication Alter Bacterial Community Composition and Aquifer Redox Conditions

2015 ◽  
Vol 81 (20) ◽  
pp. 7114-7124 ◽  
Author(s):  
Kenly A. Hiller ◽  
Kenneth H. Foreman ◽  
David Weisman ◽  
Jennifer L. Bowen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
16S Rrna ◽  
Bacterial Community Composition ◽  
Environmental Parameters ◽  
Permeable Reactive Barriers ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Reactive Barriers

ABSTRACTPermeable reactive barriers (PRBs) consist of a labile carbon source that is positioned to intercept nitrate-laden groundwater to prevent eutrophication. Decomposition of carbon in the PRB drives groundwater anoxic, fostering microbial denitrification. Such PRBs are an ideal habitat to examine microbial community structure under high-nitrate, carbon-replete conditions in coastal aquifers. We examined a PRB installed at the Waquoit Bay National Estuarine Research Reserve in Falmouth, MA. Groundwater within and below the PRB was depleted in oxygen compared to groundwater at sites upgradient and at adjacent reference sites. Nitrate concentrations declined from a high of 25 μM upgradient and adjacent to the barrier to <0.1 μM within the PRB. We analyzed the total and active bacterial communities filtered from groundwater flowing through the PRB using amplicons of 16S rRNA and of the 16S rRNA genes. Analysis of the 16S rRNA genes collected from the PRB showed that the total bacterial community had high relative abundances of bacteria thought to have alternative metabolisms, such as fermentation, including candidate phyla OD1, OP3, TM7, and GN02. In contrast, the active bacteria had lower abundances of many of these bacteria, suggesting that the bacterial taxa that differentiate the PRB groundwater community were not actively growing. Among the environmental variables analyzed, dissolved oxygen concentration explained the largest proportion of total community structure. There was, however, no significant correlation between measured environmental parameters and the active microbial community, suggesting that controls on the active portion may differ from the community as a whole.

scholarly journals Spatial and Temporal Analysis of the Microbial Community in Slow Sand Filters Used for Treating Horticultural Irrigation Water

2003 ◽  
Vol 69 (4) ◽  
pp. 2116-2125 ◽  
Author(s):  
Leo A. Calvo-Bado ◽  
Tim R. Pettitt ◽  
Nick Parsons ◽  
Geoff M. Petch ◽  
J. Alun W. Morgan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
16S Rrna ◽  
Plant Pathogen ◽  
Temporal Structure ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Global Changes ◽  
Rrna Gene ◽  
Microbial Composition

ABSTRACT An experimental slow sand filter (SSF) was constructed to study the spatial and temporal structure of a bacterial community suppressive to an oomycete plant pathogen, Phytophthora cryptogea. Passage of water through the mature sand column resulted in complete removal of zoospores of the plant pathogen. To monitor global changes in the microbial community, bacterial and fungal numbers were estimated on selective media, direct viable counts of fungal spores were made, and the ATP content was measured. PCR amplification of 16S rRNA genes and denaturing gradient gel electrophoresis (DGGE) were used to study the dynamics of the bacterial community in detail. The top layer (1 cm) of the SSF column was dominated by a variable and active microbial population, whereas the middle (50 cm) and bottom (80 cm) layers were dominated by less active and diverse bacterial populations. The major changes in the microbial populations occurred during the first week of filter operation, and these populations then remained to the end of the study. Spatial and temporal nonlinear mapping of the DGGE bands provided a useful visual representation of the similarities between SSF samples. According to the DGGE profile, less than 2% of the dominating bands present in the SSF column were represented in the culturable population. Sequence analysis of DGGE bands from all depths of the SSF column indicated that a range of bacteria were present, with 16S rRNA gene sequences similar to groups such as Bacillus megaterium, Cytophaga, Desulfovibrio, Legionella, Rhodococcus rhodochrous, Sphingomonas, and an uncharacterized environmental clone. This study describes the characterization of the performance, and microbial composition, of SSFs used for the treatment of water for use in the horticultural industry. Utilization of naturally suppressive population of microorganisms either directly or by manipulation of the environment in an SSF may provide a more reproducible control method for the future.

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