Early response of methanogenic archaea to H2 as evaluated by metagenomics and metatranscriptomics

Abstract Background The molecular machinery of the complex microbiological cell factory of biomethane production is not fully understood. One of the process control elements is the regulatory role of hydrogen (H2). Reduction of carbon dioxide (CO2) by H2 is rate limiting factor in methanogenesis, but the community intends to keep H2 concentration low in order to maintain the redox balance of the overall system. H2 metabolism in methanogens becomes increasingly important in the Power-to-Gas renewable energy conversion and storage technologies. Results The early response of the mixed mesophilic microbial community to H2 gas injection was investigated with the goal of uncovering the first responses of the microbial community in the CH4 formation and CO2 mitigation Power-to-Gas process. The overall microbial composition changes, following a 10 min excessive bubbling of H2 through the reactor, was investigated via metagenome and metatranscriptome sequencing. The overall composition and taxonomic abundance of the biogas producing anaerobic community did not change appreciably 2 hours after the H2 treatment, indicating that this time period was too short to display differences in the proliferation of the members of the microbial community. There was, however, a substantial increase in the expression of genes related to hydrogenotrophic methanogenesis of certain groups of Archaea. As an early response to H2 exposure the activity of the hydrogenotrophic methanogenesis in the genus Methanoculleus was upregulated but the hydrogenotrophic pathway in genus Methanosarcina was downregulated. The RT-qPCR data corroborated the metatranscriptomic Results H2 injection also altered the metabolism of a number of microbes belonging in the kingdom Bacteria. Many Bacteria possess the enzyme sets for the Wood-Ljungdahl pathway. These and the homoacetogens are partners for syntrophic community interactions between the distinct kingdoms of Archaea and Bacteria. Conclusions External H2 regulates the functional activity of certain Bacteria and Archaea. The syntrophic cross-kingdom interactions in H2 metabolism are important for the efficient operation of the Power-to-Gas process. Therefore, mixed communities are recommended for the large scale Power-to-Gas process rather than single hydrogenotrophic methanogen strains. Fast and reproducible response from the microbial community can be exploited in turn-off and turn-on of the Power-to-Gas microbial cell factories.

Download Full-text

Early response of methanogenic archaea to H2 as evaluated by metagenomics and metatranscriptomics

10.21203/rs.3.rs-368581/v1 ◽

2021 ◽

Author(s):

Balázs Kakuk ◽

Roland Wirth ◽

Gergely Maróti ◽

Szuhaj Márk ◽

Gábor Rakhely ◽

...

Keyword(s):

Microbial Community ◽

Large Scale ◽

Methanogenic Archaea ◽

Redox Balance ◽

Early Response ◽

Limiting Factor ◽

Cell Factory ◽

Microbial Composition ◽

Cell Factories ◽

Power To Gas

Abstract Background. The detailed molecular machinery of the complex microbiological cell factory of biogas/biomethane production is not fully understood. One of the main puzzling process control elements is the formation, consumption and regulatory role of hydrogen (H2). Reduction of carbon dioxide (CO2) by H2 is rate limiting factor in methanogenesis, but the community intends to keep H2 concentration low in order to maintain the redox balance of the overall system. H2 metabolism in methanogens becomes increasingly important in the Power-to-Gas renewable energy conversion and storage technologies. Results. The early response of the mixed mesophilic microbial community to H2 gas injection was investigated with the goal of uncovering the first responses of the microbial community in the CH4 formation and CO2 mitigation Power-to-Gas process. The overall microbial composition changes, following a 10 min H2 injection by excessive bubbling of H2 through the reactor, was investigated via metagenome and metatranscriptome sequencing. The overall composition and taxonomic abundance of the biogas producing anaerobic community did not change appreciably two hours after the H2 treatment, indicating that this time period was too short to display differences in the proliferation of the members of the microbial community. There was, however, a substantial increase in the expression of genes related to hydrogenotrophic methanogenesis of certain groups of Archaea. H2 injection also altered the metabolism of a number of microbes belonging in the kingdom Bacteria. The importance of syntrophic cross-kingdom interactions in H2 metabolism and the effects on the related Power-to-Gas process are discussed. Conclusion s. External H2 regulates the functional activity of certain Bacteria and Archaea. Mixed communities are recommended for the large scale Power-to-Gas process rather than single hydrogenotrophic methanogen strains. Fast and reproducible response from the microbial community can be exploited in turn-off and turn-on of the Power-to-Gas microbial cell factories.

Download Full-text

Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

Animal Microbiome ◽

10.1186/s42523-021-00074-8 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Sesilje Weiss ◽

David Taggart ◽

Ian Smith ◽

Kristofer M. Helgen ◽

Raphael Eisenhofer

Keyword(s):

Microbial Community ◽

Reproductive Cycle ◽

Tammar Wallaby ◽

The Body ◽

Rrna Gene ◽

Microbial Composition ◽

Birth Canal ◽

Gram Positive Bacteria ◽

Rigorous Framework ◽

The 16S Rrna Gene

Abstract Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

Download Full-text

Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

Microorganisms ◽

10.3390/microorganisms9020211 ◽

2021 ◽

Vol 9 (2) ◽

pp. 211

Author(s):

Jie Gao ◽

Miao Liu ◽

Sixue Shi ◽

Ying Liu ◽

Yu Duan ◽

...

Keyword(s):

Microbial Community ◽

High Throughput Sequencing ◽

Carbon Fixation ◽

Microbial Community Composition ◽

Ecosystem Functions ◽

Microbial Composition ◽

Wetland Ecosystems ◽

Soil Microbial ◽

Geochemical Properties ◽

Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

Download Full-text

Root traits and microbial community interactions in relation to phosphorus availability and acquisition, with particular reference to Brassica

Frontiers in Plant Science ◽

10.3389/fpls.2014.00027 ◽

2014 ◽

Vol 5 ◽

Cited By ~ 46

Author(s):

Paul J. Hunter ◽

Grahams R. Teakle ◽

Gary D. Bending

Keyword(s):

Microbial Community ◽

Root Traits ◽

Phosphorus Availability ◽

Community Interactions

Download Full-text

Nanocellulose-based mechanically stable immobilization matrix for enhanced ethylene production: A framework for photosynthetic solid-state cell factories

Green Chemistry ◽

10.1039/d1gc00502b ◽

2021 ◽

Author(s):

Ville Rissanen ◽

Sindhujaa Vajravel ◽

Sergey Kosourov ◽

Suvi Arola ◽

Eero Kontturi ◽

...

Keyword(s):

Solid State ◽

Ethylene Production ◽

Cell Immobilization ◽

Cell Factory ◽

Cell Factories ◽

Solid State Cell ◽

Immobilization Matrix

Cell immobilization is a promising approach to create efficient photosynthetic cell factories for sustainable chemicals production. Here, we demonstrate a novel photosynthetic solid-state cell factory design for sustainable biocatalytic ethylene...

Download Full-text

Ethanol, BTEX and microbial community interactions in E-blend contaminated soil slurry

International Biodeterioration & Biodegradation ◽

10.1016/j.ibiod.2009.01.005 ◽

2009 ◽

Vol 63 (6) ◽

pp. 654-666 ◽

Cited By ~ 9

Author(s):

Akvile Lawrence ◽

Susanne Jonsson ◽

Gunnar Börjesson

Keyword(s):

Microbial Community ◽

Contaminated Soil ◽

Soil Slurry ◽

Community Interactions

Download Full-text

Computational Analysis of Dynamic Light Exposure of Unicellular Algal Cells in a Flat-Panel Photobioreactor to Support Light-Induced CO2 Bioprocess Development

Frontiers in Microbiology ◽

10.3389/fmicb.2021.639482 ◽

2021 ◽

Vol 12 ◽

Author(s):

Nicolò S. Vasile ◽

Alessandro Cordara ◽

Giulia Usai ◽

Angela Re

Keyword(s):

Light Transmission ◽

Light Exposure ◽

Model Organism ◽

Cell Factory ◽

Bioprocess Development ◽

Cultivation Conditions ◽

Flat Panel ◽

Modeling Framework ◽

Cell Factories ◽

Cell Trajectories

Cyanobacterial cell factories trace a vibrant pathway to climate change neutrality and sustainable development owing to their ability to turn carbon dioxide-rich waste into a broad portfolio of renewable compounds, which are deemed valuable in green chemistry cross-sectorial applications. Cell factory design requires to define the optimal operational and cultivation conditions. The paramount parameter in biomass cultivation in photobioreactors is the light intensity since it impacts cellular physiology and productivity. Our modeling framework provides a basis for the predictive control of light-limited, light-saturated, and light-inhibited growth of the Synechocystis sp. PCC 6803 model organism in a flat-panel photobioreactor. The model here presented couples computational fluid dynamics, light transmission, kinetic modeling, and the reconstruction of single cell trajectories in differently irradiated areas of the photobioreactor to relate key physiological parameters to the multi-faceted processes occurring in the cultivation environment. Furthermore, our analysis highlights the need for properly constraining the model with decisive qualitative and quantitative data related to light calibration and light measurements both at the inlet and outlet of the photobioreactor in order to boost the accuracy and extrapolation capabilities of the model.

Download Full-text

Effect of Pyroligneous Acid on the Microbial Community Composition and Plant Growth-Promoting Bacteria (PGPB) in Soils

Soil Systems ◽

10.3390/soilsystems6010010 ◽

2022 ◽

Vol 6 (1) ◽

pp. 10

Author(s):

Anithadevi Kenday Sivaram ◽

Logeshwaran Panneerselvan ◽

Kannappar Mukunthan ◽

Mallavarapu Megharaj

Keyword(s):

Microbial Community ◽

Plant Growth ◽

Microbial Diversity ◽

Growth And Yield ◽

Rrna Gene ◽

Plant Growth Promoting Bacteria ◽

Microbial Composition ◽

Pyroligneous Acid ◽

Plant Growth Promoting ◽

Growth Promoting

Pyroligneous acid (PA) is often used in agriculture as a plant growth and yield enhancer. However, the influence of PA application on soil microorganisms is not often studied. Therefore, in this study, we investigated the effect of PA (0.01–5% w/w in soil) on the microbial diversity in two different soils. At the end of eight weeks of incubation, soil microbial community dynamics were determined by Illumina-MiSeq sequencing of 16S rRNA gene amplicons. The microbial composition differed between the lower (0.01% and 0.1%) and the higher (1% and 5%) concentration in both PA spiked soils. The lower concentration of PA resulted in higher microbial diversity and dehydrogenase activity (DHA) compared to the un-spiked control and the soil spiked with high PA concentrations. Interestingly, PA-induced plant growth-promoting bacterial (PGPB) genera include Bradyrhizobium, Azospirillum, Pseudomonas, Mesorhizobium, Rhizobium, Herbaspiriluum, Acetobacter, Beijerinckia, and Nitrosomonas at lower concentrations. Additionally, the PICRUSt functional analysis revealed the predominance of metabolism as the functional module’s primary component in both soils spiked with 0.01% and 0.1% PA. Overall, the results elucidated that PA application in soil at lower concentrations promoted soil DHA and microbial enrichment, particularly the PGPB genera, and thus have great implications for improving soil health.

Download Full-text

Compared the Microbiota Profiles between Samples from Bronchoalveolar Lavage and Endotracheal Aspirates in Severe Pneumonia: A Real-World Experience

Journal of Clinical Medicine ◽

10.3390/jcm11020327 ◽

2022 ◽

Vol 11 (2) ◽

pp. 327

Author(s):

Yeong-Nan Cheng ◽

Wei-Chih Huang ◽

Chen-Yu Wang ◽

Pin-Kuei Fu

Keyword(s):

Microbial Community ◽

Bronchoalveolar Lavage ◽

Microbial Community Composition ◽

Severe Pneumonia ◽

Metagenomic Sequencing ◽

Microbial Composition ◽

Icu Patients ◽

Mechanically Ventilated ◽

The Difference ◽

New Onset

Lower respiratory tract sampling from endotracheal aspirate (EA) and bronchoalveolar lavage (BAL) are both common methods to identify pathogens in severe pneumonia. However, the difference between these two methods in microbiota profiles remains unclear. We compared the microbiota profiles of pairwise EA and BAL samples in ICU patients with respiratory failure due to severe pneumonia. We prospectively enrolled 50 ICU patients with new onset of pneumonia requiring mechanical ventilation. EA and BAL were performed on the first ICU day, and samples were analyzed for microbial community composition via 16S rRNA metagenomic sequencing. Pathogens were identified in culture medium from BAL samples in 21 (42%) out of 50 patients. No difference was observed in the antibiotic prescription pattern, ICU mortality, or hospital mortality between BAL-positive and BAL-negative patients. The microbiota profiles in the EA and BAL samples are similar with respect to diversity, microbial composition, and microbial community correlations. The antibiotic treatment regimen was rarely changed based on the BAL findings. The samples from BAL did not provide more information than EA in the microbiota profiles. We suggest that EA is more useful than BAL for microbiome identification in mechanically ventilated patients.

Download Full-text