Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors

Talbot, Guylaine; Topp, Edward; Palin, Marie‐France; Massé, Daniel I.

doi:10.1016/j.watres.2007.08.003

Cited by 131 publications

(91 citation statements)

References 183 publications

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“…Diversity indices can then be calculated, such as richness (the number of OTUs per sample), evenness (the measure of the relative abundance of the different OTUs), and Shannon index, to define the diversity of a microbial community (see ref. 162 for a recent review of molecular methods and methods of analyses). Rarefaction curves are then usually generated by plotting the cumulative numbers of unique OTUs retrieved as the number of screened clones increases 66) .…”

Section: Retrieving Datamentioning

confidence: 99%

“…Statistical tools are used to relate species abundance in a community to environmental conditions (reviewed in refs. 67,111,162), species richness and sample coverage calculations can be performed with programs such as EstimateS (http://viceroy.eeb.uconn.edu/EstimateS), SPADE (species prediction and diversity estimation, http://chao.stat. nthu.edu.tw/softwareCE.html), LIBSHUFF (http://whitman.…”

Section: Retrieving Datamentioning

confidence: 99%

“…・Evaluate the taxonomic attribution of each tag in order to try to figure out the ecological role of each bacteria and the functioning of the community as a whole. Over time there has been numerous reviews of the methods available for studying microbial diversity 13,25,41,42,46,64,65,67,73,83,86,98,107,117,124,131,135,143,162,166,167,171,180,186) . Each method may have advantages and pitfalls, and there has been a tendency in recent years to simultaneously use several approaches, in order to obtain an extended view of the bacterial populations of complex ecosystems because some abundant species can be not retrieved by one of the methods 35,38,78,91) .…”

Section: Introductionmentioning

confidence: 99%

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Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity

Christen

2008

Microb. Environ.

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Roughly estimating the diversity of life has for a long time been seen as a challenge. Sequences obtained from the environment by direct amplification are now seen as the sole mean to provide information for at least 99% of the prokaryotes in natural communities. Recent massive parallel sequencing technologies now allow to sequence nearly every sequence resulting from such amplification. Are we ready to deal with such a deluge of data? Using three recent publications (16S rRNA genes amplification in soil and seawater followed by massive parallel sequencing) as case examples, this review analyses the state of the field.

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Section: Retrieving Datamentioning

confidence: 99%

Section: Retrieving Datamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity

Christen

2008

Microb. Environ.

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“…For ATP measurements, biomass samples were prepared from a membrane coupon (2x2.5 cm 2 ) using the destructive extraction method. A set volume of biomass sample (300 µL) was mixed with 50 µL of the reagent in FISH can hybridise targeted microbes with fluorescently labelled oligonucleotide probes and was applied to provide visual examination and quantification for the targeted microbes [120,121]. FISH were performed as described in Amann et al [122].…”

Section: Adenosine Tri-phosphate (Atp)mentioning

confidence: 99%

Biofouling control of reverse osmosis membranes using free nitrous acid

Filloux¹,

Wang²,

Pidou³

et al.

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Reverse osmosis (RO) membranes have been widely applied in membrane filtration processes for water purification, since the high selective RO membranes are designed to reject all materials with particle diameter larger than 10 angstrom (Å) [1]. However, this optimal selectivity leads to fouling that can greatly affect the performance and productivity of RO membranes. Biofouling remains as one of the major operational problems in RO processes and is caused by unwanted deposit and growth of microorganisms on the membrane. Numerous biofouling control strategies have been developed to restore the performance of RO membranes, but none of them are able to prevent or remove biofouling completely. A novel cleaning technique using a weak and monobasic acid (pKa=3.34, 25℃) named free nitrous acid (FNA) in combined with hydrogen dioxide (H 2 O 2 ) was proposed.The effects of FNA with or without H 2 O 2 on biofouling of RO membranes were investigated in Chapter 4, five RO membranes with different degree of biofouling were cleaned using FNA has achieved higher biomass removal than NaOH for both heavily fouled (86-96% versus 41-83%) and moderately fouled (92-95% against 89-92%) membranes, respectively.In accordance to the biomass removal, 6-32% of viable cells remained on the moderately fouled RO membranes under the impact of FNA cleaning (pH 3), whereas 38-58% of viable cells stayed on the heavily fouled RO membranes. These results revealed that FNA cleaning is more effective for moderately fouled membranes, implying that early cleaning for biofouling is preferable. Although applying FNA alone, or combining it with H2O2 have shown better efficiency at biofouling removal than NaOH, the cleaning efficiency has not been significantly improved (<1% of enhancement) by adding H 2 O 2 to FNA cleaning solutions. The effects of FNA on scaling of RO membranes were also studied using the same cleaning protocol developed for biofouling control. The results showed that FNA solutions at pH 2.0 and 3.0 were as efficient as conventional cleaning acids (hydrochloric acid and citric acid). The scaling layers which contain 32.4±1.7 g/cm 2 of calcium were completely removed by all acidic cleaning solutions. Based on the results, FNA is shown to be a promising ii cleaning agent for RO membrane biofouling and scaling removal.Further investigation focused on the effectiveness of FNA for biofouling prevention in RO processes (Chapter 5). The results showed that weekly FNA cleanings were unable to prevent fouling in the RO filtration systems, as the hydraulic performances (permeability and salt rejection) of RO membranes have gradually declined over two to three weeks filtration period.Although FNA cleaning was able to restore the permeability of RO membranes for one to two days, continuing declined permeability implied that the fouling rate was greater than the inhibition rate of FNA. The results of prevention tests also showed that FNA was more efficient at biomass inactivation and removal. The biomass contents and viable cells of the fouli...

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“…High abundance of Syntrophomonas was generally detected with higher archaeal abundance in anaerobic reactors (Regueiro et al, 2012), engaging in obligate syntrophic propionate oxidation (Talbot et al, 2008). Syntrophomonas was also detected with high abundance in anaerobic sludge treating slaughterhouse wastewater with high fats level (Cammarota et al, 2013) and thought to be the major anaerobic bacterium oxidising butyrate and long-chain fatty acids to acetate and hydrogen through β-oxidation (Pereira et al, 2002).…”

Section: Microbial Architecturementioning

confidence: 99%

Microbial Ecology of Fermentative Microbes in Anaerobic Granules

Yang¹

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School of Chemical EngineeringII"|"P a g e " % AbstractGranules are large, self-supporting biofilms that form naturally in high-rate anaerobic treatment systems and are extremely important to reactor functionality. The biofilm structure has functional and phylogenetic layering, important both scientifically and to function.Fermenters, found on the surface of anaerobic granules, are associated with granule strength and uptake of the primary substrate. Compared to acetogens and methanogens, very limited work has been done on fermenters, particularly in granules. Due to their high diversity and difficulty in selective isolation, fermenters are best studied through culture-independent techniques. Until now, the microbial distribution could only be analysed through sectioning and microscopic analysis with fluorescent in situ hybridization. The whole granule could be analysed by DNA extraction and microbial community profiling methods but this did not provide spatial information. This thesis develops a method to remove microbes selectively from successive spatial layers through hydraulic shearing and demonstrates its application on anaerobic granules of three different types (collected from brewery, cannery and dairy wastewater treatment plants). Outer layers, in particular, could be selectively sheared as confirmed by FISH and TRFLP. Further analysis with 454 pyrosequencing showed that a shift in dominant population from presumptive fermenters (such as Bacteroidales and Anaerolinea) in outer layers to syntrophs (such as Syntrophomonas and Geobacter) in inner layers, with progressive changes through the depth. The method was further leveraged through covariance based deep metagenomic sequencing, with metagenomic analysis used so far to align phylogenetic information. This leveraged the shear based method to provide covariance information for the metagenomic analysis. Shear based phylogenetic and metagenomic aligned well internally and with cryosection-FISH analysis. Information provided could be used with more specific probes (particularly Bacteroidales and Anaerolinea) to confirm that these organisms were key fermenters and highly abundant in outer layers. This study indicated that fermenters were a relatively diverse but discrete population within the granule. Further analysis of the metagenomic information is required to identify roles of specific microbes. The phylogenetic approach was also used in a reactor study with different feeds (gelatine, glucose, VFA) to identify how the microbial population shifted during growth of fermenters. While physical strength was not influenced, the III"|"P a g e " % dominant fermentative groups were strongly impacted by the feed matrix, and inner layer community less changed, but still substantially affected.

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Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors

Cited by 131 publications

References 183 publications

Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity

Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity

Biofouling control of reverse osmosis membranes using free nitrous acid

Microbial Ecology of Fermentative Microbes in Anaerobic Granules

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