Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

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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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Population Abundance of Potentially Pathogenic Organisms in Intestinal Microbiome of Jungle Crow (Corvus macrorhynchos) Shown with 16S rRNA Gene-Based Microbial Community Analysis

BioMed Research International ◽

10.1155/2013/438956 ◽

2013 ◽

Vol 2013 ◽

pp. 1-5 ◽

Cited By ~ 8

Author(s):

Isamu Maeda ◽

Mohammad Shohel Rana Siddiki ◽

Tsutomu Nozawa-Takeda ◽

Naoki Tsukahara ◽

Yuri Tani ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Pathogenic Bacteria ◽

Community Analysis ◽

Microbial Community Analysis ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Jungle Crow ◽

Corvus Macrorhynchos

Jungle Crows (Corvus macrorhynchos) prefer human habitats because of their versatility in feeding accompanied with human food consumption. Therefore, it is important from a public health viewpoint to characterize their intestinal microbiota. However, no studies have been involved in molecular characterization of the microbiota based on huge and reliable number of data acquisition. In this study, 16S rRNA gene-based microbial community analysis coupled with the next-generation DNA sequencing techniques was applied to the taxonomic classification of intestinal microbiome for three jungle crows. Clustering of the reads into 130 operational taxonomic units showed that at least 70% of analyzed sequences for each crow were highly homologous toEimeriasp., which belongs to the protozoan phylumApicomplexa. The microbiotas of three crows also contained potentially pathogenic bacteria with significant percentages, such as the generaCampylobacterandBrachyspira. Thus, the profiling of a large number of 16S rRNA gene sequences in crow intestinal microbiomes revealed the high-frequency existence or vestige of potentially pathogenic microorganisms.

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Universal 16s rRNA Primers BD1 For Soil Microbial Community Analysis

Ecological genetics ◽

10.17816/ecogen4432-37 ◽

2006 ◽

Vol 4 (4) ◽

pp. 32-37

Author(s):

Elisaveta V Korostik ◽

Alexander G Pinaev ◽

Gulnar A Akhtemova ◽

Evgeniy E Andronov

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Community Analysis ◽

Microbial Community Analysis ◽

Rrna Gene ◽

Community Studies ◽

Bacterial Isolates ◽

16S Rrna Gene Sequences ◽

Soil Microbial ◽

16S Rrna Clone Library

New universal 16S rRNa primers were constructed and tested. These primers allow identifying correct taxonomic position of bacterial isolates and were shown to be useful in microbial community studies. The primers enable to detect the vast majority of unique 16S rRNa gene sequences. In the study 160 restriction types were found in 16S rRNa clone library (190 clones).

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Evaluation of DESS as a storage medium for microbial community analysis

10.7287/peerj.preprints.27041v1 ◽

2018 ◽

Author(s):

Kevin M Lee ◽

Madison Adams ◽

Jonathan L Klassen

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Microbial Ecology ◽

Microbial Community Structure ◽

Community Analysis ◽

Microbial Community Analysis ◽

Ant Colonies ◽

And Storage ◽

Phosphate Buffered Saline

Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test the ability of these preservatives to maintain the structure of fungus garden microbial communities. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.

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Microbial Community Dynamics of an Urban Drinking Water Distribution System Subjected to Phases of Chloramination and Chlorination Treatments

Applied and Environmental Microbiology ◽

10.1128/aem.01892-12 ◽

2012 ◽

Vol 78 (22) ◽

pp. 7856-7865 ◽

Cited By ~ 87

Author(s):

Chiachi Hwang ◽

Fangqiong Ling ◽

Gary L. Andersen ◽

Mark W. LeChevallier ◽

Wen-Tso Liu

Keyword(s):

Drinking Water ◽

Microbial Community ◽

Microbial Communities ◽

Distribution Systems ◽

Water Distribution ◽

Microbial Populations ◽

Rrna Gene ◽

Source Water ◽

Content Type ◽

Drinking Water Distribution

ABSTRACTWater utilities in parts of the U.S. control microbial regrowth in drinking water distribution systems (DWDS) by alternating postdisinfection methods between chlorination and chloramination. To examine how this strategy influences drinking water microbial communities, an urban DWDS (population ≅ 40,000) with groundwater as the source water was studied for approximately 2 years. Water samples were collected at five locations in the network at different seasons and analyzed for their chemical and physical characteristics and for their microbial community composition and structure by examining the 16S rRNA gene via terminal restriction fragment length polymorphism and DNA pyrosequencing technology. Nonmetric multidimension scaling and canonical correspondence analysis of microbial community profiles could explain >57% of the variation. Clustering of samples based on disinfection types (free chlorine versus combined chlorine) and sampling time was observed to correlate to the shifts in microbial communities. Sampling location and water age (<21.2 h) had no apparent effects on the microbial compositions of samples from most time points. Microbial community analysis revealed that among major core populations,Cyanobacteria,Methylobacteriaceae,Sphingomonadaceae, andXanthomonadaceaewere more abundant in chlorinated water, andMethylophilaceae,Methylococcaceae, andPseudomonadaceaewere more abundant in chloraminated water. No correlation was observed with minor populations that were detected frequently (<0.1% of total pyrosequences), which were likely present in source water and survived through the treatment process. Transient microbial populations includingFlavobacteriaceaeandClostridiaceaewere also observed. Overall, reversible shifts in microbial communities were especially pronounced with chloramination, suggesting stronger selection of microbial populations from chloramines than chlorine.

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Microbial Community Stratification Linked to Utilization of Carbohydrates and Phosphorus Limitation in a Boreal Peatland at Marcell Experimental Forest, Minnesota, USA

Applied and Environmental Microbiology ◽

10.1128/aem.00205-14 ◽

2014 ◽

Vol 80 (11) ◽

pp. 3518-3530 ◽

Cited By ~ 61

Author(s):

Xueju Lin ◽

Malak M. Tfaily ◽

J. Megan Steinweg ◽

Patrick Chanton ◽

Kaitlin Esson ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Hot Spot ◽

Microbial Community Composition ◽

Phosphorus Limitation ◽

Rrna Gene ◽

Content Type ◽

Gene Abundance ◽

P Limitation

ABSTRACTThis study investigated the abundance, distribution, and composition of microbial communities at the watershed scale in a boreal peatland within the Marcell Experimental Forest (MEF), Minnesota, USA. Through a close coupling of next-generation sequencing, biogeochemistry, and advanced analytical chemistry, a biogeochemical hot spot was revealed in the mesotelm (30- to 50-cm depth) as a pronounced shift in microbial community composition in parallel with elevated peat decomposition. The relative abundance ofAcidobacteriaand theSyntrophobacteraceae, including known hydrocarbon-utilizing genera, was positively correlated with carbohydrate and organic acid content, showing a maximum in the mesotelm. The abundance ofArchaea(primarily crenarchaeal groups 1.1c and 1.3) increased with depth, reaching up to 60% of total small-subunit (SSU) rRNA gene sequences in the deep peat below the 75-cm depth. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by theMethanosarcinalesin the mesotelm, while hydrogen-utilizing methanogens predominated in the deeper catotelm. RNA-derived pyrosequence libraries corroborated DNA sequence data to indicate that the above-mentioned microbial groups are metabolically active in the mid-depth zone. Fungi showed a maximum in rRNA gene abundance above the 30-cm depth, which comprised only an average of 0.1% of total bacterial and archaeal rRNA gene abundance, indicating prokaryotic dominance. Ratios of C to P enzyme activities approached 0.5 at the acrotelm and catotelm, indicating phosphorus limitation. In contrast, P limitation pressure appeared to be relieved in the mesotelm, likely due to P solubilization by microbial production of organic acids and C-P lyases. Based on path analysis and the modeling of community spatial turnover, we hypothesize that P limitation outweighs N limitation at MEF, and microbial communities are structured by the dominant shrub,Chamaedaphne calyculata, which may act as a carbon source for major consumers in the peatland.

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Microbial community analysis of biofilters reveals a dominance of either comammox Nitrospira or archaea as ammonia oxidizers in freshwater aquaria

10.1101/2021.11.24.468873 ◽

2021 ◽

Author(s):

Michelle M McKnight ◽

Josh D Neufeld

Keyword(s):

Microbial Communities ◽

Ammonia Oxidation ◽

16S Rrna Gene Sequencing ◽

Community Analysis ◽

Microbial Community Analysis ◽

Ammonia Oxidizer ◽

Future Research ◽

Rrna Gene ◽

Ammonia Oxidizing Bacteria ◽

Ammonia Oxidizers

Nitrification by aquarium biofilters transforms toxic ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Ammonia oxidation is mediated by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizing (comammox) Nitrospira. Prior to the discovery of comammox Nitrospira, previous research revealed that AOA dominate among ammonia oxidizers in freshwater biofilters. Here, we characterized the composition of aquarium filter microbial communities and quantified the abundance of all three known groups of ammonia oxidizers. Aquarium biofilter and water samples were collected from representative freshwater and saltwater systems in Southwestern Ontario, Canada. Using extracted DNA, we performed 16S rRNA gene sequencing and quantitative PCR (qPCR) to assess community composition and quantify the abundance of amoA genes, respectively. Our results show that aquarium biofilter microbial communities were consistently represented by putative heterotrophs of the Proteobacteria and Bacteroides phyla, with distinct profiles associated with fresh versus saltwater biofilters. Among nitrifiers, comammox Nitrospira amoA genes were detected in all 38 freshwater aquarium biofilter samples and were the most abundant ammonia oxidizer in 30 of these samples, with the remaining biofilters dominated by AOA, based on amoA gene abundances. In saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. These results demonstrate that comammox Nitrospira play an important role in biofilter nitrification that has been previously overlooked and such microcosms are useful for exploring the ecology of nitrification for future research.

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Evaluation of DESS as a storage medium for microbial community analysis

10.7287/peerj.preprints.27041 ◽

2018 ◽

Author(s):

Kevin M Lee ◽

Madison Adams ◽

Jonathan L Klassen

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Microbial Ecology ◽

Microbial Community Structure ◽

Community Analysis ◽

Microbial Community Analysis ◽

Ant Colonies ◽

And Storage ◽

Phosphate Buffered Saline

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PCR Amplification-Independent Methods for Detection of Microbial Communities by the High-Density Microarray PhyloChip

Applied and Environmental Microbiology ◽

10.1128/aem.05262-11 ◽

2011 ◽

Vol 77 (18) ◽

pp. 6313-6322 ◽

Cited By ~ 54

Author(s):

Kristen M. DeAngelis ◽

Cindy H. Wu ◽

Harry R. Beller ◽

Eoin L. Brodie ◽

Romy Chakraborty ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Pcr Amplification ◽

Community Analysis ◽

High Density ◽

Microbial Community Analysis ◽

Taxon Richness ◽

Tropical Forest Soil ◽

Global Biogeochemical Cycles ◽

Direct Hybridization

ABSTRACTEnvironmental microbial community analysis typically involves amplification by PCR, despite well-documented biases. We have developed two methods of PCR-independent microbial community analysis using the high-density microarray PhyloChip: direct hybridization of 16S rRNA (dirRNA) or rRNA converted to double-stranded cDNA (dscDNA). We compared dirRNA and dscDNA communities to PCR-amplified DNA communities using a mock community of eight taxa, as well as experiments derived from three environmental sample types: chromium-contaminated aquifer groundwater, tropical forest soil, and secondary sewage in seawater. Community profiles by both direct hybridization methods showed differences that were expected based on accompanying data but that were missing in PCR-amplified communities. Taxon richness decreased in RNA compared to that in DNA communities, suggesting a subset of 20% in soil and 60% in groundwater that is active; secondary sewage showed no difference between active and inactive populations. Direct hybridization of dscDNA and RNA is thus a viable alternative to PCR-amplified microbial community analysis, providing identification of the active populations within microbial communities that attenuate pollutants, drive global biogeochemical cycles, or proliferate disease states.

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Microbial community analysis with a specific statistical approach after a record breaking snowfall in Southern Italy

Annals of Microbiology ◽

10.1186/s13213-020-01604-6 ◽

2020 ◽

Vol 70 (1) ◽

Author(s):

Pamela Monaco ◽

Fabio Divino ◽

Gino Naclerio ◽

Antonio Bucci

Keyword(s):

Microbial Communities ◽

Statistical Approach ◽

Biological Diversity ◽

Southern Italy ◽

Bacterial Species ◽

Species Level ◽

Microbial Community Analysis ◽

Rrna Gene ◽

Additional Tool ◽

Snow Samples

Abstract Purpose Snow and ice ecosystems present unexpectedly high microbial abundance and diversity. Although arctic and alpine snow environments have been intensively investigated from a microbiological point of view, few studies have been conducted in the Apennines. Accordingly, the main purpose of this research was to analyze the microbial communities of the snow collected in two different locations of Capracotta municipality (Southern Italy) after a snowfall record occurred on March 2015 (256 cm of snow in less than 24 h). Methods Bacterial communities were analyzed by the Next-Generation Sequencing techniques. Furthermore, a specific statistical approach for taxonomic hierarchy data was introduced, both for the assessment of diversity within microbial communities and the comparison between different microbiotas. In general, diversity and similarity indices are more informative when computed at the lowest level of the taxonomic hierarchy, the species level. This is not the case with microbial data, for which the species level is not necessarily the most informative. Indeed, the possibility to detect a large number of unclassified records at every level of the hierarchy (even at the top) is very realistic due to both the partial knowledge about the cultivable fraction of microbial communities and limitations to taxonomic assignment connected to the quality and completeness of the 16S rRNA gene reference databases. Thus, a global approach considering information from the whole taxonomic hierarchy was adopted in order to obtain a more consistent assessment of the biodiversity. Result The main phyla retrieved in the investigated snow samples were Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Interestingly, DNA from bacteria adapted to thrive at low temperatures, but also from microorganisms normally associated with other habitats, whose presence in the snow could be justified by wind-transport, was found. Biomolecular investigations and statistical data analysis showed relevant differences in terms of biodiversity, composition, and distribution of bacterial species between the studied snow samples. Conclusion The relevance of this research lies in the expansion of knowledge about microorganisms associated with cold environments in contexts poorly investigated such as the Italian Apennines, and in the development of a global statistical approach for the assessment of biological diversity and similarity of microbial communities as an additional tool to be usefully combined with the barcoding methods.

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