Correction to: Hill-based dissimilarity indices and null models for analysis of microbial community assembly.

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Hill-based dissimilarity indices and null models for analysis of microbial community assembly.

BACKGROUND: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases, and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models. RESULTS: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems. CONCLUSIONS: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package ( https://github.com/omvatten/qdiv ). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines. Video Abstract.

Response to starvation and microbial community composition in microbial fuel cells enriched on different electron donors.

In microbial fuel cells (MFCs), microorganisms generate electrical current by oxidizing organic compounds. MFCs operated with different electron donors harbour different microbial communities, and it is unknown how that affects their response to starvation. We analysed the microbial communities in acetate- and glucose-fed MFCs and compared their responses to 10 days starvation periods. Each starvation period resulted in a 4.2 ± 1.4% reduction in electrical current in the acetate-fed MFCs and a 10.8 ± 3.9% reduction in the glucose-fed MFCs. When feed was resumed, the acetate-fed MFCs recovered immediately, whereas the glucose-fed MFCs required 1 day to recover. The acetate-fed bioanodes were dominated by Desulfuromonas spp. converting acetate into electrical current. The glucose-fed bioanodes were dominated by Trichococcus sp., functioning as a fermenter, and a member of Desulfuromonadales, using the fermentation products to generate electrical current. Suspended biomass and biofilm growing on non-conductive regions within the MFCs had different community composition than the bioanodes. However, null models showed that homogenizing dispersal of microorganisms within the MFCs affected the community composition, and in the glucose-fed MFCs, the Trichococcus sp. was abundant in all locations. The different responses to starvation can be explained by the more complex pathway requiring microbial interactions to convert glucose into electrical current.

A variety of hydrogenotrophic enrichment cultures catalyse cathodic reactions.

Biocathodes where living microorganisms catalyse reduction of CO2 can potentially be used to produce valuable chemicals. Microorganisms harbouring hydrogenases may play a key role for biocathode performance since H2 generated on the electrode surface can act as an electron donor for CO2 reduction. In this study, the possibility of catalysing cathodic reactions by hydrogenotrophic methanogens, acetogens, sulfate-reducers, denitrifiers, and acetotrophic methanogens was investigated. The cultures were enriched from an activated sludge inoculum and performed the expected metabolic functions. All enrichments formed distinct microbial communities depending on their electron donor and electron acceptor. When the cultures were added to an electrochemical cell, linear sweep voltammograms showed a shift in current generation close to the hydrogen evolution potential (-1 V versus SHE) with higher cathodic current produced at a more positive potential. All enrichment cultures except the denitrifiers were also used to inoculate biocathodes of microbial electrolysis cells operated with H+ and bicarbonate as electron acceptors and this resulted in current densities between 0.1-1 A/m2. The microbial community composition of biocathodes inoculated with different enrichment cultures were as different from each other as they were different from their suspended culture inoculum. It was noteworthy that Methanobacterium sp. appeared on all the biocathodes suggesting that it is a key microorganism catalysing biocathode reactions.

Effect of Start-Up Strategies and Electrode Materials on Carbon Dioxide Reduction on Biocathodes.

The enrichment of CO2-reducing microbial biocathodes is challenging. Previous research has shown that a promising approach could be to first enrich bioanodes and then lower the potential so the electrodes are converted into biocathodes. However, the effect of such a transition on the microbial community on the electrode has not been studied. The goal of this study was thus to compare the start-up of biocathodes from preenriched anodes with direct start-up from bare electrodes and to investigate changes in microbial community composition. The effect of three electrode materials on the long-term performance of the biocathodes was also investigated. In this study, preenrichment of acetate-oxidizing bioanodes did not facilitate the start-up of biocathodes. It took about 170 days for the preenriched electrodes to generate substantial cathodic current, compared to 83 days for the bare electrodes. Graphite foil and carbon felt cathodes produced higher current at the beginning of the experiment than did graphite rods. However, all electrodes produced similar current densities at the end of the over 1-year-long study (2.5 A/m2). Methane was the only product detected during operation of the biocathodes. Acetate was the only product detected after inhibition of the methanogens. Microbial community analysis showed that Geobacter sp. dominated the bioanodes. On the biocathodes, the Geobacter sp. was succeeded by Methanobacterium spp., which made up more than 80% of the population. After inhibition of the methanogens, Acetobacterium sp. became dominant on the electrodes (40% relative abundance). The results suggested that bioelectrochemically generated H2 acted as an electron donor for CO2 reduction.IMPORTANCE In microbial electrochemical systems, living microorganisms function as catalysts for reactions on the anode and/or the cathode. There is a variety of potential applications, ranging from wastewater treatment and biogas generation to production of chemicals. Systems with biocathodes could be used to reduce CO2 to methane, acetate, or other high-value chemicals. The technique can be used to convert solar energy to chemicals. However, enriching biocathodes that are capable of CO2 reduction is more difficult and less studied than enriching bioanodes. The effect of different start-up strategies and electrode materials on the microbial communities that are enriched on biocathodes has not been studied. The purpose of this study was to investigate two different start-up strategies and three different electrode materials for start-up and long-term operation of biocathodes capable of reducing CO2 to valuable biochemicals.

Effects of storage on mixed-culture biological electrodes.

Storage methods are important to preserve the viability and biochemical characteristics of microbial cultures between experiments or during periods when bioreactors are inactive. Most of the research on storage has focused on isolates; however, there is an increasing interest in methods for mixed cultures, which are of relevance in environmental biotechnology. The purpose of this study was to investigate the effect of different storage methods on electrochemically active enrichment cultures. Acetate-oxidizing bioanodes generating a current density of about 5 A m(-2) were enriched in a microbial electrolysis cell. The effect of five weeks of storage was evaluated using electrochemical techniques and microbial community analysis. Storage by refrigeration resulted in quicker re-activation than freezing in 10% glycerol, while the bioelectrochemical activity was entirely lost after storage using dehydration. The results showed that the bioelectrochemical activity of bioanodes stored at low temperature could be retained. However, during the re-activation period the bioanodes only recovered 75% of the current density generated before storage and the bacterial communities were different in composition and more diverse after storage than before.

Sorption and release of organics by primary, anaerobic, and aerobic activated sludge mixed with raw municipal wastewater.

New activated sludge processes that utilize sorption as a major mechanism for organics removal are being developed to maximize energy recovery from wastewater organics, or as enhanced primary treatment technologies. To model and optimize sorption-based activated sludge processes, further knowledge about sorption of organics onto sludge is needed. This study compared primary-, anaerobic-, and aerobic activated sludge as sorbents, determined sorption capacity and kinetics, and investigated some characteristics of the organics being sorbed. Batch sorption assays were carried out without aeration at a mixing velocity of 200 rpm. Only aerobic activated sludge showed net sorption of organics. Sorption of dissolved organics occurred by a near-instantaneous sorption event followed by a slower process that obeyed 1st order kinetics. Sorption of particulates also followed 1st order kinetics but there was no instantaneous sorption event; instead there was a release of particles upon mixing. The 5-min sorption capacity of activated sludge was 6.5±10.8 mg total organic carbon (TOC) per g volatile suspend solids (VSS) for particulate organics and 5.0±4.7 mgTOC/gVSS for dissolved organics. The observed instantaneous sorption appeared to be mainly due to organics larger than 20 kDa in size being sorbed, although molecules with a size of about 200 Da with strong UV absorbance at 215-230 nm were also rapidly removed.