scholarly journals Hydrogen as a Co-electron Donor for Chain Elongation With Complex Communities

2021 ◽  
Vol 9 ◽  
Author(s):  
Flávio C. F. Baleeiro ◽  
Sabine Kleinsteuber ◽  
Heike Sträuber
Keyword(s):  
Microbial Communities ◽  
Electron Donor ◽  
Amplicon Sequencing ◽  
Sensu Stricto ◽  
Lessons Learned ◽  
Electron Donors ◽  
Chain Elongation ◽  
Medium Chain ◽  
16S Rrna Amplicon Sequencing ◽  
Hydrogenotrophic Methanogenesis

Electron donor scarcity is seen as one of the major issues limiting economic production of medium-chain carboxylates from waste streams. Previous studies suggest that co-fermentation of hydrogen in microbial communities that realize chain elongation relieves this limitation. To better understand how hydrogen co-feeding can support chain elongation, we enriched three different microbial communities from anaerobic reactors (A, B, and C with ascending levels of diversity) for their ability to produce medium-chain carboxylates from conventional electron donors (lactate or ethanol) or from hydrogen. In the presence of abundant acetate and CO2, the effects of different abiotic parameters (pH values in acidic to neutral range, initial acetate concentration, and presence of chemical methanogenesis inhibitors) were tested along with the enrichment. The presence of hydrogen facilitated production of butyrate by all communities and improved production of i-butyrate and caproate by the two most diverse communities (B and C), accompanied by consumption of acetate, hydrogen, and lactate/ethanol (when available). Under optimal conditions, hydrogen increased the selectivity of conventional electron donors to caproate from 0.23 ± 0.01 mol e–/mol e– to 0.67 ± 0.15 mol e–/mol e– with a peak caproate concentration of 4.0 g L–1. As a trade-off, the best-performing communities also showed hydrogenotrophic methanogenesis activity by Methanobacterium even at high concentrations of undissociated acetic acid of 2.9 g L–1 and at low pH of 4.8. According to 16S rRNA amplicon sequencing, the suspected caproate producers were assigned to the family Anaerovoracaceae (Peptostreptococcales) and the genera Megasphaera (99.8% similarity to M. elsdenii), Caproiciproducens, and Clostridium sensu stricto 12 (97–100% similarity to C. luticellarii). Non-methanogenic hydrogen consumption correlated to the abundance of Clostridium sensu stricto 12 taxa (p < 0.01). If a robust methanogenesis inhibition strategy can be found, hydrogen co-feeding along with conventional electron donors can greatly improve selectivity to caproate in complex communities. The lessons learned can help design continuous hydrogen-aided chain elongation bioprocesses.

scholarly journals Machine Learning-assisted Identification of Bioindicators Predicts Medium-chain Carboxylate Production Performance of an Anaerobic Mixed Culture

2020 ◽  
Author(s):  
Bin Liu ◽  
Heike Sträuber ◽  
Joao Saraiva ◽  
Hauke Harms ◽  
Sandra Godinho Silva ◽  
...  
Keyword(s):  
Machine Learning ◽  
16S Rrna ◽  
Retention Time ◽  
Hydraulic Retention Time ◽  
Amplicon Sequencing ◽  
Production Performance ◽  
Chain Elongation ◽  
Sequencing Data ◽  
Medium Chain ◽  
16S Rrna Amplicon Sequencing

Abstract Background: The ability to quantitatively predict ecophysiological functions of microbial communities provides an important step to engineer microbiota for desired functions related to specific biochemical conversions. Here, we present the quantitative prediction of medium-chain carboxylate production in two continuous anaerobic bioreactors from 16S rRNA gene dynamics in enrichment cultures. Results: By progressively shortening the hydraulic retention time from 8 days to 2 days with different temporal schemes in both bioreactors operated for 211 days, we achieved higher productivities and yields of the target products n-caproate and n-caprylate. The datasets generated from each bioreactor were applied independently for training and testing in machine learning. A predictive model was generated by employing the random forest algorithm using 16S rRNA amplicon sequencing data. More than 90% accuracy in the prediction of n-caproate and n-caprylate productivities was achieved. Four inferred bioindicators belonging to the genera Olsenella, Lactobacillus, Syntrophococcus and Clostridium IV suggest their relevance to the higher carboxylate productivity at shorter hydraulic retention time. The recovery of metagenome-assembled genomes of these bioindicators confirmed their genetic potential to perform key steps of medium-chain carboxylate production.Conclusions: Shortening the hydraulic retention time of the continuous bioreactor systems allows to shape the communities with desired chain elongation functions. Using machine-learning, we demonstrated that 16S rRNA amplicon sequencing data can be used to predict bioreactor process performance quantitatively and accurately. Characterising and harnessing bioindicators holds promise to manage reactor microbiota towards selection of the target processes. Our mathematical framework is transferrable to other ecosystem processes and 3 microbial systems where community dynamics is linked to key functions. The general methodology can be adapted to data types of other functional categories such as genes, transcripts, proteins or metabolites.

scholarly journals Linking nitrogen load to the structure and function of wetland soil and rhizosphere microbial communities

2017 ◽  
Author(s):  
Eric R Hester ◽  
Sarah F. Harpenslager ◽  
Josepha MH van Diggelen ◽  
Leon L Lamers ◽  
Mike SM Jetten ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Greenhouse Gas Emissions ◽  
Greenhouse Gas ◽  
Amplicon Sequencing ◽  
N Fertilization ◽  
Wetland Soil ◽  
N Availability ◽  
Gas Emissions ◽  
16S Rrna Amplicon Sequencing ◽  
N Input

AbstractWetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, N2O and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning such as control of greenhouse gas emissions. Therefore it is important to understand how increased N input into pristine wetlands affects the composition and activity of micro-organisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangle the effects of N fertilization on the microbial community in bulk soil and the rhizosphere ofJuncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations withJ. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA amplicon sequencing and metagenomics, we determined that the bacterial orders Opitutales, Subgroup-6 Acidobacteria and Sphingobacteriales significantly responded to high N availability and we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, severely altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities.

scholarly journals Deciphering the Influence of Multiple Anthropogenic Inputs on Taxonomic and Functional Profiles of the Microbial Communities in Yitong River, Northeast China

2021 ◽  
Author(s):  
Ying Zhang ◽  
Yang Huo ◽  
Zhiruo Zhang ◽  
Suiyi Zhu ◽  
Wei Fan ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Northeast China ◽  
Environmental Changes ◽  
Quantitative Polymerase Chain Reaction ◽  
Amplicon Sequencing ◽  
Fecal Indicator ◽  
16S Rrna Amplicon Sequencing ◽  
Anthropogenic Inputs ◽  
Wwtp Effluent ◽  
The Impact

Abstract We conducted physicochemical parameters analysis, 16S rRNA amplicon sequencing and real-time quantitative polymerase chain reaction to explore the impact of human inputs on the bacterioplankton communities within a tributary of the largest river flowing through a megacity in northeast China. Agriculture largely accounted for the alteration of diversity and functions of the microbial communities. Furthermore, nutrients were significantly declined at the reservoir outlet, and WWTP effluent discharge caused changes in the river microbial community. NH3-N and NO3--N were the main environmental factors that drive the shift of the bacteria community, and rare taxa played a more important role in the response to environmental changes compared with the abundant ones. The occurrence of the human-specific fecal indicator was mostly derived from agriculture, and its increase in relative abundance was observed in the effluent. Thus, our study provides guidance for ecological assessment and management of rivers by revealing the response pattern of river bacterioplankton to multiple types of anthropogenic stressors.

scholarly journals Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major)

2020 ◽  
Author(s):  
Kasun H Bodawatta ◽  
Katerina Puzejova ◽  
Katerina Sam ◽  
Michael Poulsen ◽  
Knud A. Jønsson
Keyword(s):  
Microbial Communities ◽  
Digestive Tract ◽  
Wild Bird ◽  
Anthropogenic Impacts ◽  
Parus Major ◽  
Amplicon Sequencing ◽  
Cloacal Swab ◽  
Non Invasive ◽  
16S Rrna Amplicon Sequencing ◽  
Microbiome Research

Abstract Background Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in alcohol provide promising avenues to increase our understanding of wild bird microbiomes, provided that they accurately portray natural microbial community compositions. To investigate this assertion, we used 16S rRNA amplicon sequencing of Great tit (Parus major) gut microbiomes to compare 1) microbial communities obtained from dissected digestive tract regions and cloacal swabs, and 2) microbial communities obtained from freshly dissected gut regions and from samples preserved in alcohol for two weeks or two months, respectively. Results We found no significant differences in alpha diversities in communities of different gut regions and cloacal swabs (except in OTU richness between the dissected cloacal region and the cloacal swabs), or between fresh and alcohol preserved samples. However, we did find significant differences in beta diversity and community composition of cloacal swab samples compared to different gut regions. Despite these community-level differences, swab samples qualitatively captured the majority of the bacterial diversity throughout the gut better than any single compartment. Bacterial community compositions of alcohol-preserved specimens did not differ significantly from freshly dissected samples, although some low-abundant taxa were lost in the alcohol preserved specimens. Conclusions Our findings suggest that cloacal swabs, similar to non-invasive fecal sampling, qualitatively depict the gut microbiota composition without having to collect birds to extract the full digestive tract. Secondly, the satisfactory depiction of gut microbial communities in alcohol preserved samples opens up for the possibility of using an enormous resource readily available through museum collections to characterize bird gut microbiomes. The use of extensive museum specimen collections of birds for microbial gut analyses would allow for investigations of temporal patterns of wild bird gut microbiomes, including the potential effects of climate change and anthropogenic impacts. Overall, the utilization of cloacal swabs and museum alcohol specimens can positively impact bird gut microbiome research to help increase our understanding of the role and evolution of wild bird hosts and gut microbial communities.

scholarly journals Product Inhibition and pH Affect Stoichiometry and Kinetics of Chain Elongating Microbial Communities in Sequencing Batch Bioreactors

2021 ◽  
Vol 9 ◽  
Author(s):  
Maximilienne Toetie Allaart ◽  
Gerben Roelandt Stouten ◽  
Diana Z. Sousa ◽  
Robbert Kleerebezem
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Short Chain Fatty Acids ◽  
Product Inhibition ◽  
Chain Elongation ◽  
Rrna Gene ◽  
Specific Substrate ◽  
Substrate Uptake ◽  
Ph Values ◽  
Kinetics Of

Anaerobic microbial communities can produce carboxylic acids of medium chain length (e.g., caproate, caprylate) by elongating short chain fatty acids through reversed β-oxidation. Ethanol is a common electron donor for this process. The influence of environmental conditions on the stoichiometry and kinetics of ethanol-based chain elongation remains elusive. Here, a sequencing batch bioreactor setup with high-resolution off-gas measurements was used to identify the physiological characteristics of chain elongating microbial communities enriched on acetate and ethanol at pH 7.0 ± 0.2 and 5.5 ± 0.2. Operation at both pH-values led to the development of communities that were highly enriched (>50%, based on 16S rRNA gene amplicon sequencing) in Clostridium kluyveri related species. At both pH-values, stably performing cultures were characterized by incomplete substrate conversion and decreasing biomass-specific hydrogen production rates during an operational cycle. The process stoichiometries obtained at both pH-values were different: at pH 7.0, 71 ± 6% of the consumed electrons were converted to caproate, compared to only 30 ± 5% at pH 5.5. Operating at pH 5.5 led to a decrease in the biomass yield, but a significant increase in the biomass-specific substrate uptake rate, suggesting that the organisms employ catabolic overcapacity to deal with energy losses associated to product inhibition. These results highlight that chain elongating conversions rely on a delicate balance between substrate uptake- and product inhibition kinetics.

scholarly journals Localization of bacterial communities within gut compartments across Cephalotes turtle ants

2021 ◽  
Author(s):  
Peter J. Flynn ◽  
Catherine L. D’Amelio ◽  
Jon G. Sanders ◽  
Jacob A. Russell ◽  
Corrie S. Moreau
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Digestive Tract ◽  
Bacterial Communities ◽  
Evolutionary History ◽  
Amplicon Sequencing ◽  
Caste Differentiation ◽  
Animal Group ◽  
16S Rrna Amplicon Sequencing ◽  
Host Phylogeny

Microbial communities within the animal digestive tract often provide important functions for their hosts. The composition of eukaryotes' gut bacteria can be shaped by host diet, vertical bacterial transmission, and physiological variation within the digestive tract. In several ant taxa, recent findings have demonstrated that nitrogen provisioning by symbiotic bacteria makes up for deficiencies in herbivorous diets. Using 16S rRNA amplicon sequencing and qPCR, this study examined bacterial communities at a fine scale across one such animal group, the turtle ant genus Cephalotes. We analyzed the composition and colonization density across four portions of the digestive tract to understand how bacterial diversity is structured across gut compartments, potentially allowing for specific metabolic functions of benefit to the host. In addition, we aimed to understand if caste differentiation or host relatedness influences the gut bacterial communities of Cephalotes ants. Microbial communities were found to vary strongly across Cephalotes gut compartments in ways that transcend both caste and host phylogeny. Despite this, caste and host phylogeny still have detectable effects. We demonstrated microbial community divergence across gut compartments, possibly due to the varying function of each gut compartment for digestion. IMPORTANCE Gut compartments play an important role in structuring the microbial community within individual ants. The gut chambers of the turtle ant digestive tract differ remarkably in symbiont abundance and diversity. Furthermore, caste type explains some variation in the microbiome composition. Finally, the evolutionary history of the Cephalotes species structures the microbiome in our study, which elucidates a trend in which related ants maintain related microbiomes, conceivably owing to co-speciation. Amazingly, gut compartment-specific signatures of microbial diversity, relative abundance, composition, and abundance have been conserved over Cephalotes evolutionary history, signifying that this symbiosis has been largely stable for over 50 million years.

scholarly journals 16S rRNA Amplicon Sequencing of Microbial Biofilms from Marsberg Copper Mine, Germany

2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Sania Arif ◽  
Elias Schliekmann ◽  
Michael Hoppert
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Water Bodies ◽  
Rhenish Massif ◽  
Copper Mine ◽  
Selective Enrichment ◽  
Microbial Biofilms ◽  
16S Rrna Amplicon Sequencing

ABSTRACT The 16S rRNA amplicons from biofilms inhabiting rocks near various water bodies of Marsberg Copper Mine (Rhenish Massif, Germany) reveal the diversity of their microbial communities. The abundance of Chloroflexi and Cyanobacteria taxa in the biofilms near leachate streams indicated the selective enrichment of Ktedonobacteria and Oxyphotobacteria members.

scholarly journals Instability and Stasis Among the Microbiome of Seagrass Leaves, Roots and Rhizomes, and Nearby Sediments Within a Natural pH Gradient

2021 ◽  
Author(s):  
Raymond B. Banister ◽  
Melbert T. Schwarz ◽  
Maoz Fine ◽  
Kim B. Ritchie ◽  
Erinn M. Muller
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Elevated Temperatures ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Ph Gradient ◽  
Ecological Value ◽  
Seagrass Meadows ◽  
16S Rrna Amplicon Sequencing ◽  
Natural Ph Gradient

AbstractSeagrass meadows are hotspots of biodiversity with considerable economic and ecological value. The health of seagrass ecosystems is influenced in part by the makeup and stability of their microbiome, but microbiome composition can be sensitive to environmental change such as nutrient availability, elevated temperatures, and reduced pH. The objective of the present study was to characterize the bacterial community of the leaves, bulk samples of roots and rhizomes, and proximal sediment of the seagrass species Cymodocea nodosa along the natural pH gradient of Levante Bay, Vulcano Island, Italy. The bacterial community was determined by characterizing the 16S rRNA amplicon sequencing and analyzing the operational taxonomic unit classification of bacterial DNA within samples. Statistical analyses were used to explore how life-long exposure to different pH/pCO2 conditions may be associated with significant differences in microbial communities, dominant bacterial classes, and microbial diversity within each plant section and sediment. The microbiome of C. nodosa significantly differed among all sample types and site-specific differences were detected within sediment and root/rhizome microbial communities, but not the leaves. These results show that C. nodosa leaves have a consistent microbial community even across a pH range of 8.15 to 6.05. The ability for C. nodosa to regulate and maintain microbial structure may indicate a semblance of resilience within these vital ecosystems under projected changes in environmental conditions such as ocean acidification.

scholarly journals Successional patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic Ridge

2019 ◽  
Author(s):  
Sabine Haalboom ◽  
David M. Price ◽  
Furu Mienis ◽  
Judith D. L. van Bleijswijk ◽  
Henko C. de Stigter ◽  
...  
Keyword(s):  
Trace Metals ◽  
Microbial Communities ◽  
Water Column ◽  
Hydrothermal Vent ◽  
Amplicon Sequencing ◽  
Buoyant Plume ◽  
Hydrothermal Plume ◽  
Mining Sites ◽  
16S Rrna Amplicon Sequencing ◽  
Neutrally Buoyant

Abstract. Hydrothermal vent fields found at mid-ocean ridges emit hydrothermal fluids which disperse as neutrally buoyant plumes. From these fluids seafloor massive sulfides (SMS) deposits are formed which are being explored as possible new mining sites for (trace) metals and rare earth elements (REE). It has been suggested that during mining activities large amounts of suspended matter will appear in the water column due to excavation processes, and due to discharge of mining waste from the surface vessel. Understanding how natural hydrothermal plumes evolve as they spread away from their source and how they affect their surrounding environment may provide some analogies for the behaviour of the dilute distal part of chemically enriched mining plumes. This study on the extensive Rainbow hydrothermal plume, observed up to 25 km downstream from the vent site, enabled us to investigate how microbial communities change in the presence of a natural plume. The (trace) metal and REE content of suspended particulate matter (SPM) was determined using HR-ICP mass spectrometry and the microbial communities of the neutrally buoyant plume, above plume-, below plume-, and near-bottom water and sediment were characterised by using 16S rRNA amplicon sequencing methods. Both vertically in the water column and horizontally along the neutrally buoyant plume, geochemical and biological changes were evident as the neutrally buoyant plume stood out by its enrichments in (trace) metals and REEs, of which the concentrations changed as the plume aged. This was also reflected in the background pelagic system as Epsilonproteobacteria started to dominate and the biodiversity appeared to reduce with distance away from the Rainbow hydrothermal vent field. The Rainbow hydrothermal plume provides a geochemically enriched natural environment, which is a heterogeneous, dynamic habitat that is conducive to ecological changes in a short time span.

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