Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities

Albertsen, Mads; Karst, Søren Michael; Ziegler, Anja; Kirkegaard, Rasmus Hansen; Nielsen, Per Halkjær

doi:10.1371/journal.pone.0132783

Cited by 462 publications

(400 citation statements)

References 41 publications

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“…Chao1 species richness estimates and Shannon diversity indices were calculated with Phyloseq. Results were visualized with the R packages Phyloseq and ampvis (Albertsen et al, 2015) (R version 3.2.4). Sequence data including raw reads, quality scores and mapping data have been deposited in the NCBI Sequence Read Archive (SRA) database with the BioProject number PRJNA395419.…”

Section: Sequence Analysismentioning

confidence: 99%

Hot Spring Microbial Community Composition, Morphology, and Carbon Fixation: Implications for Interpreting the Ancient Rock Record

2017

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Microbial communities in hydrothermal systems exist in a range of macroscopic morphologies including stromatolites, mats, and filaments. The architects of these structures are typically autotrophic, serving as primary producers. Structures attributed to microbial life have been documented in the rock record dating back to the Archean including recent reports of microbially-related structures in terrestrial hot springs that date back as far as 3.5 Ga. Microbial structures exhibit a range of complexity from filaments to more complex mats and stromatolites and the complexity impacts preservation potential. As a result, interpretation of these structures in the rock record relies on isotopic signatures in combination with overall morphology and paleoenvironmental setting. However, the relationships between morphology, microbial community composition, and primary productivity remain poorly constrained. To begin to address this gap, we examined community composition and carbon fixation in filaments, mats, and stromatolites from the Greater Obsidian Pool Area (GOPA) of the Mud Volcano Area, Yellowstone National Park, WY. We targeted morphologies dominated by bacterial phototrophs located in close proximity within the same pool which are exposed to similar geochemistry as well as bacterial mat, algal filament and chemotrophic filaments from nearby springs. Our results indicate (i) natural abundance δ 13 C values of biomass from these features (−11.0 to −24.3‰) are similar to those found in the rock record; (ii) carbon uptake rates of photoautotrophic communities is greater than chemoautotrophic; (iii) oxygenic photosynthesis, anoxygenic photosynthesis, and chemoautotrophy often contribute to carbon fixation within the same morphology; and (iv) increasing phototrophic biofilm complexity corresponds to a significant decrease in rates of carbon fixation-filaments had the highest uptake rates whereas carbon fixation by stromatolites was significantly lower. Our data highlight important differences in primary productivity between structures despite indistinguishable δ 13 C values of the biomass. Furthermore, low primary productivity by stromatolites compared to other structures underscores the need to consider a larger role for microbial mats and filaments in carbon fixation and O 2 generation during the Archean and Proterozoic.

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Section: Sequence Analysismentioning

confidence: 99%

Hot Spring Microbial Community Composition, Morphology, and Carbon Fixation: Implications for Interpreting the Ancient Rock Record

2017

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“…However, despite much research effort into different DNA extraction protocols, it seems unlikely that there will ever be a perfect protocol. The biases introduced in DNA extraction can only be minimised not circumvented (Guo and Zhang, 2013;Albertsen et al, 2015). The aim of this section is to give a brief overview of the steps involved in DNA extraction and to make general recommendations when working with activated sludge.…”

Section: General Considerationsmentioning

confidence: 99%

“…The aim of this section is to give a brief overview of the steps involved in DNA extraction and to make general recommendations when working with activated sludge. In addition, a protocol optimized for the use in activated sludge is presented, based on the protocol developed by Albertsen et al (2015).…”

Section: General Considerationsmentioning

confidence: 99%

“…The difficult nature of activated sludge presents a challenge for several of these approaches due to different kinds of inhibition (Tullis and Rubin, 1980). However, mechanical lysis has proven very robust and does not suffer from inhibition effects (Salonen et al, 2010;Guo and Zhang, 2013;Albertsen et al, 2015). The lysis of cells is often carried out in solutions with detergents and surfactants that support the disruption and removal of cell membrane constituents such as lipids by a subsequent centrifugation step.…”

Section: Cell Lysismentioning

confidence: 99%

“…The protocol is based on the FastDNA spin kit for soil protocol (MP Biomedicals) with some modifications, mainly streamlining and longer bead beating, as published by Albertsen et al (2015).…”

Section: Optimised Dna Extraction From Wastewater Activated Sludgementioning

confidence: 99%

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Experimental Methods in Wastewater Treatment

Loosdrecht¹,

Nielsen²,

López-Vázquez³

et al. 2016

Water Intelligence Online

137

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PrefaceWastewater treatment is a core technology for water resources protection and reuse, as is clearly demonstrated by the great success of its consequent implementation in many countries worldwide. During the last decennia scientific research has made vast progress in understanding the complex and interdisciplinary aspects of the biological, biochemical, chemical and mechanical processes involved. It can be concluded that the global application of existing knowledge and experience in wastewater treatment technology will represent a cornerstone in future water management, as expressed in the Strategic Development Goals accepted by the UN in September 2015.Only about one fifth of the wastewater produced globally is currently being adequately treated. To achieve the goal for sustainable water management by 2030 would require extra wastewater treatment facilities for about 600,000 people each day. I am convinced that this book will make its own significant contribution to meeting this ambitious goal.In the near future, most of the global population will live in cities and in low and middle-income countries, where most wastewater is not adequately treated. Probably the most limiting factor in achieving the goals for sustainable water management is the lack of qualified, well-trained professionals, able to comprehend the scientific research results and transfer them into practice. It is therefore of prime importance to make currently available scientific advances and proven experiences in wastewater treatment technology applications easily accessible worldwide. This was one of the drivers for the development of this book, which represents an innovative contribution to help overcome such a capacity development challenge. The book is most definitely expected to contribute to bridging the gaps between the science and technology, and their practical applications.The great collection of authors and reviewers represents an interdisciplinary team of globally acknowledged experts. The book will therefore make a major contribution to establishing a common professional language, enhancing global communication between wastewater professionals. In addition, the authors have linked the description of the scientific basis for wastewater treatment processes with a video-based online course for the training of students, researchers, engineers, laboratory technicians and treatment plant operators, demonstrating commonly accepted experimentation procedures and their application for lab-, pilot-, and full-scale treatment plant operation.From the perspective of the IWA this book also has the great potential to enhance the development of a new generation of researchers and enable them to communicate on a global scale and beyond their specific field of expertise. Both aspects are urgently needed to develop adapted solutions for specific local conditions and to make them globally available for implementation.There has been a trend for some time that scientific research and practice have been growing apart from each other. Part of the rea...

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Neopolyploidy has variable effects on the diversity and composition of the wild strawberry microbiome

Anneberg,

Cullen,

O'Neill

et al. 2024

American J of Botany

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PremiseWhole‐genome duplication (neopolyploidy) can instantly differentiate the phenotype of neopolyploids from their diploid progenitors. These phenotypic shifts in organs such as roots and leaves could also differentiate the way neopolyploids interact with microbial species. While some studies have addressed how specific microbial interactions are affected by neopolyploidy, we lack an understanding of how genome duplication affects the diversity and composition of microbial communities.MethodsWe performed a common garden experiment with multiple clones of artificially synthesized autotetraploids and their ancestral diploids, derived from 13 genotypes of wild strawberry, Fragaria vesca. We sequenced epiphytic bacteria and fungi from roots and leaves and characterized microbial communities and leaf functional traits.ResultsAutotetraploidy had no effect on bacterial alpha diversity of either organ, but it did have a genotype‐dependent effect on the diversity of fungi on leaves. In contrast, autotetraploidy restructured the community composition of leaf bacteria and had a genotype‐dependent effect on fungal community composition in both organs. The most differentially abundant bacterial taxon on leaves belonged to the Sphingomonas, while a member of the Trichoderma was the most differentially abundant fungal taxon on roots. Ploidy‐induced change in leaf size was strongly correlated with a change in bacterial but not fungal leaf communities.ConclusionsGenome duplication can immediately alter aspects of the plant microbiome, but this effect varies by host genotype and bacterial and fungal community. Expanding these studies to wild settings where plants are exposed continuously to microbes are needed to confirm the patterns observed here.

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Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities

Cited by 462 publications

References 41 publications

Hot Spring Microbial Community Composition, Morphology, and Carbon Fixation: Implications for Interpreting the Ancient Rock Record

Hot Spring Microbial Community Composition, Morphology, and Carbon Fixation: Implications for Interpreting the Ancient Rock Record

Experimental Methods in Wastewater Treatment

Neopolyploidy has variable effects on the diversity and composition of the wild strawberry microbiome

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