Assessing biological stability in a porous groundwater aquifer of a riverbank filtration system: combining traditional cultivation-based and emerging cultivation-independent in situ and predictive methods

AbstractRiverbank filtration systems are important drinking water resources. Aquifers of riverbank filtration systems are subjected to considerable dynamics concerning the quantity and quality of the infiltrating water. The microbiological quality is mainly jeopardized by faecal contamination of the main river. Besides, water quality can be impacted by growth of natural water-borne bacteria due to the input of nutrients resulting in the proliferation of opportunistic pathogens, impairment of odour and taste or bio-corrosion. The occurrence of such phenomena indicates a biological instability. For highly dynamic riverbank filtration systems, it is thus of high relevance to assess the biological stability of the groundwater resource.In the present study, we applied a holistic, two-tiered concept of in situ and predictive methods to assess the biostability of the aquifer in a bank filtration system of the Danube River. We applied traditional cultivation-based and selected cultivation-independent methods—including cultivation on yeast extract and R2A agar, determination of total cell counts via fluorescence microscopy and flow cytometry, leucine incorporation and 16S rRNA gene amplicon sequencing—at critical control points along the infiltration path from the river to the abstraction well.The concentration of organic nutrients and the hydrological variability were the main controlling factors driving the biological stability of the groundwater body. Wells situated at greater distance displayed significantly lower dissolved organic carbon concentrations and a dampened hydrological influence in comparison to the well situated next to the river. Apparent discrepancies between the methods used indicated a different indicator function of the cultivation-based and cultivation-independent approaches. For complex systems, we thus recommend this new holistic concept for assessing biostability by combining in situ as well as predictive parameters and using cultivation-based and cultivation-independent methods.

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

Microorganisms ◽

10.3390/microorganisms8060936 ◽

2020 ◽

Vol 8 (6) ◽

pp. 936 ◽

Cited By ~ 2

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.

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Phylogenetic Analysis and In Situ Identification of Bacteria Community Composition in an Acidic Sphagnum Peat Bog

Applied and Environmental Microbiology ◽

10.1128/aem.72.3.2110-2117.2006 ◽

2006 ◽

Vol 72 (3) ◽

pp. 2110-2117 ◽

Cited By ~ 213

Author(s):

Svetlana N. Dedysh ◽

Timofei A. Pankratov ◽

Svetlana E. Belova ◽

Irina S. Kulichevskaya ◽

Werner Liesack

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Community Composition ◽

Significant Proportion ◽

Peat Bog ◽

Rrna Gene ◽

Bacterial Phyla ◽

Cell Counts ◽

Novel Strategy

ABSTRACT The Bacteria community composition in an acidic Sphagnum peat bog (pH 3.9 to 4.5) was characterized by a combination of 16S rRNA gene clone library analysis, rRNA-targeted fluorescence in situ hybridization (FISH), and cultivation. Among 84 environmental 16S rRNA gene clones, a set of only 16 cloned sequences was closely related (≥95% similarity) to taxonomically described organisms. Main groups of clones were affiliated with the Acidobacteria (24 clones), Alphaproteobacteria (20), Verrucomicrobia (13), Actinobacteria (8), Deltaproteobacteria (4), Chloroflexi (3), and Planctomycetes (3). The proportion of cells that hybridized with oligonucleotide probes specific for members of the domains Bacteria (EUB338-mix) and Archaea (ARCH915 and ARC344) accounted for only 12 to 22% of the total cell counts. Up to 24% of the EUB338-positive cells could be assigned by FISH to specific bacterial phyla. Alphaproteobacteria and Planctomycetes were the most numerous bacterial groups (up to 1.3 × 107 and 1.1 × 107 cells g−1 peat, respectively). In contrast to conventional plating techniques, a novel biofilm-mediated enrichment approach allowed us to isolate some representatives of predominant Bacteria groups, such as Acidobacteria and Planctomycetes. This novel strategy has great potential to enable the isolation of a significant proportion of the peat bog bacterial diversity.

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Two Bacteria Phylotypes Are Predominant in the Suiyo Seamount Hydrothermal Plume

Applied and Environmental Microbiology ◽

10.1128/aem.70.2.1190-1198.2004 ◽

2004 ◽

Vol 70 (2) ◽

pp. 1190-1198 ◽

Cited By ~ 101

Author(s):

Michinari Sunamura ◽

Yowsuke Higashi ◽

Chiwaka Miyako ◽

Jun-ichiro Ishibashi ◽

Akihiko Maruyama

Keyword(s):

Bottom Layer ◽

Rrna Gene ◽

Phylogenetic Groups ◽

Dapi Staining ◽

Hydrothermal Plume ◽

Filtration System ◽

Group Belonging ◽

Complex Relationships ◽

Almost All

ABSTRACT Microbial diversity and populations in a hydrothermal plume that was present inside the caldera of the Suiyo Seamount, a submarine volcano on the Izu-Bonin Arc, were investigated by performing a phylogenetic analysis of the 16S rRNA gene and by using fluorescence in situ hybridization (FISH). Corresponding to transmissivity, an indicator of turbidity, the vertical total cell count as determined by 4′,6′-diamidino-2-phenylindole (DAPI) staining varied from 5.6 × 104 to 1.1 × 105 cells ml−1, and the apparent plume layer was assessed to be at a depth of 1,050 to 1,200 m inside the caldera and to contain 1.0 × 105 to 1.1 × 105 cells ml−1. From microbial samples collected in the plume by an in situ filtration system, the following two major phylogenetic groups, which were closely related to sulfur-oxidizing microbes, were obtained: the SUP05 group belonging to the gamma subclass of the Proteobacteria (13 of 20 clones) and the SUP01 group belonging to the epsilon subclass of the Proteobacteria (5 of 20 clones). Specific oligonucleotide probes for these groups (SUP05-187 and SUP01-63) were designed and were used with various water samples obtained from the Suiyo Seamount. In the apparent plume layer, up to 66% of the total counts of microbial cells were estimated to be Bacteria cells that hybridized to EUB338, and few cells were identified by the archaeal probe ARCH915. Almost all Bacteria cells were hard to identify with the known group-specific probes, such as ALF19, GAM42a, and CF319, while 88 to 90% of the Bacteria cells hybridized with SUP05-187 and >98% of them were considered members of the SUP05 and SUP01 populations. In a low-temperature vent fluid emitted from a bivalve-colonized mound, the SUP05 cells accounted for >99% of the Bacteria cells, suggesting that a portion of the plume cells originated on the surface of the seafloor at a depth of about 1,380 m. From further analysis of cell morphology (i.e., cell size and cell elongation index) we inferred that the SUP05 cells were active in the plume layer at a depth of 1,050 to 1,200 m compared to the activity in a near-bottom layer, while many elongated cells were found between these layers. These findings suggest that the morphology and distribution of SUP05 cells have complex relationships with hydrothermal activities and water circulation. Although growth and production rates remain to be defined, we concluded that this Suiyo Seamount caldera has functioned as a natural continuous incubator for these two phylotypes of Bacteria in an aphotic deep-sea environment.

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Recognition of Individual Genes in Diverse Microorganisms by Cycling Primed In Situ Amplification

Applied and Environmental Microbiology ◽

10.1128/aem.71.11.7236-7244.2005 ◽

2005 ◽

Vol 71 (11) ◽

pp. 7236-7244 ◽

Cited By ~ 19

Author(s):

Takehiko Kenzaka ◽

Shigeru Tamaki ◽

Nobuyasu Yamaguchi ◽

Katsuji Tani ◽

Masao Nasu

Keyword(s):

Water Samples ◽

Bacterial Cell ◽

High Sensitivity ◽

Pond Water ◽

Specific Gene ◽

Rrna Gene ◽

Detection Rates ◽

Cell Counts ◽

Probe Set

ABSTRACT Cycling primed in situ amplification-fluorescent in situ hybridization (CPRINS-FISH) was developed to recognize individual genes in a single bacterial cell. In CPRINS, the amplicon was long single-stranded DNA and thus retained within the permeabilized microbial cells. FISH with a multiply labeled fluorescent probe set enabled significant reduction in nonspecific background while maintaining high fluorescence signals of target bacteria. The ampicillin resistance gene in Escherichia coli, chloramphenicol acetyltransferase gene in different gram-negative strains, and RNA polymerase sigma factor (rpoD) gene in Aeromonas spp. could be detected under identical permeabilization conditions. After concentration of environmental freshwater samples onto polycarbonate filters and subsequent coating of filters in gelatin, no decrease in bacterial cell numbers was observed with extensive permeabilization. The detection rates of bacterioplankton in river and pond water samples by CPRINS-FISH with a universal 16S rRNA gene primer and probe set ranged from 65 to 76% of total cell counts (mean, 71%). The concentrations of cells detected by CPRINS-FISH targeting of the rpoD genes of Aeromonas sobria and A. hydrophila in the water samples varied between 2.1 × 103 and 9.0 × 103 cells ml−1 and between undetectable and 5.1 × 102 cells ml−1, respectively. These results demonstrate that CPRINS-FISH provides a high sensitivity for microscopic detection of bacteria carrying a specific gene in natural aquatic samples.

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In Situ Iron-manganese Removal by an Oxygenated Water Injection-and-extraction Technique in a Riverbank Filtration System

The Journal of Engineering Geology ◽

10.9720/kseg.2015.3.339 ◽

2015 ◽

Vol 25 (3) ◽

pp. 339-347 ◽

Cited By ~ 4

Author(s):

Myeong-Jae Yi ◽

Jang-Hwan Cha ◽

Ho-June Jang ◽

Hyun-suk Ahn ◽

Chan Hahn ◽

...

Keyword(s):

Water Injection ◽

Riverbank Filtration ◽

Extraction Technique ◽

Manganese Removal ◽

Filtration System ◽

Oxygenated Water ◽

Iron Manganese

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“Candidatus Dechloromonas phosphoritropha” and “Ca. D. phosphorivorans”, novel polyphosphate accumulating organisms abundant in wastewater treatment systems

The ISME Journal ◽

10.1038/s41396-021-01029-2 ◽

2021 ◽

Author(s):

Francesca Petriglieri ◽

Caitlin Singleton ◽

Miriam Peces ◽

Jette F. Petersen ◽

Marta Nierychlo ◽

...

Keyword(s):

Wastewater Treatment ◽

Wastewater Treatment Plants ◽

Niche Partitioning ◽

16S Rrna Gene Sequencing ◽

Abundant Species ◽

Phosphate Removal ◽

Rrna Gene ◽

Biological Phosphorus Removal ◽

Polyphosphate Accumulating Organisms

AbstractMembers of the genus Dechloromonas are often abundant in enhanced biological phosphorus removal (EBPR) systems and are recognized putative polyphosphate accumulating organisms (PAOs), but their role in phosphate removal is still unclear. Here, we used 16S rRNA gene sequencing and fluorescence in situ hybridization (FISH) to investigate the abundance and distribution of Dechloromonas spp. in Danish and global wastewater treatment plants. The two most abundant species worldwide revealed in situ dynamics of important intracellular storage polymers, measured by FISH-Raman in activated sludge from four full-scale EBPR plants and from a lab-scale reactor fed with different substrates. Moreover, seven distinct Dechloromonas species were determined from a set of ten high-quality metagenome-assembled genomes (MAGs) from Danish EBPR plants, each encoding the potential for polyphosphate (poly-P), glycogen, and polyhydroxyalkanoates (PHA) accumulation. The two species exhibited an in situ phenotype in complete accordance with the metabolic information retrieved by the MAGs, with dynamic levels of poly-P, glycogen, and PHA during feast-famine anaerobic–aerobic cycling, legitimately placing these microorganisms among the important PAOs. They are potentially involved in denitrification showing niche partitioning within the genus and with other important PAOs. As no isolates are available for the two species, we propose the names Candidatus Dechloromonas phosphoritropha and Candidatus Dechloromonas phosphorivorans.

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Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh

Microbiome ◽

10.1186/s40168-020-00964-0 ◽

2021 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Daniel R. Leadbeater ◽

Nicola C. Oates ◽

Joseph P. Bennett ◽

Yi Li ◽

Adam A. Dowle ◽

...

Keyword(s):

Salt Marsh ◽

Salt Marshes ◽

Molecular Mechanisms ◽

Surface Sediments ◽

Gene Profiling ◽

Oxidative Enzymes ◽

Lignocellulose Degradation ◽

Rrna Gene ◽

Enzymatic Mechanisms

Abstract Background Salt marshes are major natural repositories of sequestered organic carbon with high burial rates of organic matter, produced by highly productive native flora. Accumulated carbon predominantly exists as lignocellulose which is metabolised by communities of functionally diverse microbes. However, the organisms that orchestrate this process and the enzymatic mechanisms employed that regulate the accumulation, composition and permanence of this carbon stock are not yet known. We applied meta-exo-proteome proteomics and 16S rRNA gene profiling to study lignocellulose decomposition in situ within the surface level sediments of a natural established UK salt marsh. Results Our studies revealed a community dominated by Gammaproteobacteria, Bacteroidetes and Deltaproteobacteria that drive lignocellulose degradation in the salt marsh. We identify 42 families of lignocellulolytic bacteria of which the most active secretors of carbohydrate-active enzymes were observed to be Prolixibacteracea, Flavobacteriaceae, Cellvibrionaceae, Saccharospirillaceae, Alteromonadaceae, Vibrionaceae and Cytophagaceae. These families secreted lignocellulose-active glycoside hydrolase (GH) family enzymes GH3, GH5, GH6, GH9, GH10, GH11, GH13 and GH43 that were associated with degrading Spartina biomass. While fungi were present, we did not detect a lignocellulolytic contribution from fungi which are major contributors to terrestrial lignocellulose deconstruction. Oxidative enzymes such as laccases, peroxidases and lytic polysaccharide monooxygenases that are important for lignocellulose degradation in the terrestrial environment were present but not abundant, while a notable abundance of putative esterases (such as carbohydrate esterase family 1) associated with decoupling lignin from polysaccharides in lignocellulose was observed. Conclusions Here, we identify a diverse cohort of previously undefined bacteria that drive lignocellulose degradation in the surface sediments of the salt marsh environment and describe the enzymatic mechanisms they employ to facilitate this process. Our results increase the understanding of the microbial and molecular mechanisms that underpin carbon sequestration from lignocellulose within salt marsh surface sediments in situ and provide insights into the potential enzymatic mechanisms regulating the enrichment of polyphenolics in salt marsh sediments.

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Microbiological and Geochemical Heterogeneity in an In Situ Uranium Bioremediation Field Site

Applied and Environmental Microbiology ◽

10.1128/aem.71.10.6308-6318.2005 ◽

2005 ◽

Vol 71 (10) ◽

pp. 6308-6318 ◽

Cited By ~ 172

Author(s):

Helen A. Vrionis ◽

Robert T. Anderson ◽

Irene Ortiz-Bernad ◽

Kathleen R. O'Neill ◽

Charles T. Resch ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

16S Rrna Genes ◽

Rrna Genes ◽

Acid Volatile Sulfide ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Geochemical Heterogeneity

ABSTRACT The geochemistry and microbiology of a uranium-contaminated subsurface environment that had undergone two seasons of acetate addition to stimulate microbial U(VI) reduction was examined. There were distinct horizontal and vertical geochemical gradients that could be attributed in large part to the manner in which acetate was distributed in the aquifer, with more reduction of Fe(III) and sulfate occurring at greater depths and closer to the point of acetate injection. Clone libraries of 16S rRNA genes derived from sediments and groundwater indicated an enrichment of sulfate-reducing bacteria in the order Desulfobacterales in sediment and groundwater samples. These samples were collected nearest the injection gallery where microbially reducible Fe(III) oxides were highly depleted, groundwater sulfate concentrations were low, and increases in acid volatile sulfide were observed in the sediment. Further down-gradient, metal-reducing conditions were present as indicated by intermediate Fe(II)/Fe(total) ratios, lower acid volatile sulfide values, and increased abundance of 16S rRNA gene sequences belonging to the dissimilatory Fe(III)- and U(VI)-reducing family Geobacteraceae. Maximal Fe(III) and U(VI) reduction correlated with maximal recovery of Geobacteraceae 16S rRNA gene sequences in both groundwater and sediment; however, the sites at which these maxima occurred were spatially separated within the aquifer. The substantial microbial and geochemical heterogeneity at this site demonstrates that attempts should be made to deliver acetate in a more uniform manner and that closely spaced sampling intervals, horizontally and vertically, in both sediment and groundwater are necessary in order to obtain a more in-depth understanding of microbial processes and the relative contribution of attached and planktonic populations to in situ uranium bioremediation.

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Microbial Community Analysis inside a Biooxidation Heap for Gold Recovery in Equador

Solid State Phenomena ◽

10.4028/www.scientific.net/ssp.262.135 ◽

2017 ◽

Vol 262 ◽

pp. 135-138 ◽

Cited By ~ 3

Author(s):

Carlos L. Aspiazu ◽

Paulina Aguirre ◽

Sabrina Hedrich ◽

Axel Schippers

Keyword(s):

Microbial Community ◽

Fine Fraction ◽

Community Analysis ◽

Gold Recovery ◽

Microbial Community Analysis ◽

Most Probable Number ◽

Rrna Gene ◽

Probable Number ◽

Cell Numbers ◽

Cell Counts

In a mine owned by the company Orenas S.A. (Equador), a biooxidation process for gold recovery has been developed. Refractory gold ore was crushed, milled and 500 ton of flotation concentrate was agglomerated by coating a support rock. This was piled up on a liner and the biooxidation process in the heap of 35x25x6 m3 was run for approximately 150 days. The oxidized material was subsequently removed for further processing. An outcrop allowed for depth dependent sampling of altogether 36 samples at three sites over the complete depth of 6 m. The fine fraction was removed from the host rock and sent to the laboratory for analysis of the microbial community. The pH ranged between 2.2 and 2.9. Total cell counts determined via counting under a fluorescence microscope after SYBR Green staining indicated a high microbial colonialization of the heap in all depths between 106 to 109 cells per g concentrate, however the highest cell numbers were mainly found in the upper 50 cm. Most-probable-number determination of living, acidophilic iron (II)-oxidizers for one site also revealed a decrease of cell numbers with depth (between 104 to 108 cells per g concentrate). Further molecular analyses of the community composition based on extracted DNA and 16S rRNA gene analyses by TRFLP and qPCR revealed a complex archaeal and bacterial community within the heap. It can be stated that an active community of acidophiles runs the biooxidation process in all sampled parts of the heap.

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