scholarly journals Geothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, Italy

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Nunzia Picone ◽  
Carmen Hogendoorn ◽  
Geert Cremers ◽  
Lianna Poghosyan ◽  
Arjan Pol ◽  
...  
Keyword(s):  
Microbial Community ◽  
Greenhouse Gas ◽  
Relative Abundance ◽  
Hot Spots ◽  
Microbial Community Composition ◽  
Metagenomic Analysis ◽  
Volcanic Soil ◽  
Metabolic Potential ◽  
Gas Emissions ◽  
Geothermal Activity

ABSTRACT Volcanic and geothermal environments are characterized by low pH, high temperatures, and gas emissions consisting of mainly CO2 and varied CH4, H2S, and H2 contents which allow the formation of chemolithoautotrophic microbial communities. To determine the link between the emitted gases and the microbial community composition, geochemical and metagenomic analysis were performed. Soil samples of the geothermic region Favara Grande (Pantelleria, Italy) were taken at various depths (1 to 50 cm). Analysis of the gas composition revealed that CH4 and H2 have the potential to serve as the driving forces for the microbial community. Our metagenomic analysis revealed a high relative abundance of Bacteria in the top layer (1 to 10 cm), but the relative abundance of Archaea increased with depth from 32% to 70%. In particular, a putative hydrogenotrophic methanogenic archaeon, related to Methanocella conradii, appeared to have a high relative abundance (63%) in deeper layers. A variety of [NiFe]-hydrogenase genes were detected, showing that H2 was an important electron donor for microaerobic microorganisms in the upper layers. Furthermore, the bacterial population included verrucomicrobial and proteobacterial methanotrophs, the former showing an up to 7.8 times higher relative abundance. Analysis of the metabolic potential of this microbial community showed a clear capacity to oxidize CH4 aerobically, as several genes for distinct particulate methane monooxygenases and lanthanide-dependent methanol dehydrogenases (XoxF-type) were retrieved. Analysis of the CO2 fixation pathways showed the presence of the Calvin-Benson-Bassham cycle, the Wood-Ljungdahl pathway, and the (reverse) tricarboxylic acid (TCA) cycle, the latter being the most represented carbon fixation pathway. This study indicates that the methane emissions in the Favara Grande might be a combination of geothermal activity and biological processes and further provides insights into the diversity of the microbial population thriving on CH4 and H2. IMPORTANCE The Favara Grande nature reserve on the volcanic island of Pantelleria (Italy) is known for its geothermal gas emissions and high soil temperatures. These volcanic soil ecosystems represent “hot spots” of greenhouse gas emissions. The unique community might be shaped by the hostile conditions in the ecosystem, and it is involved in the cycling of elements such as carbon, hydrogen, sulfur, and nitrogen. Our metagenome study revealed that most of the microorganisms in this extreme environment are only distantly related to cultivated bacteria. The results obtained profoundly increased the understanding of these natural hot spots of greenhouse gas production/degradation and will help to enrich and isolate the microbial key players. After isolation, it will become possible to unravel the molecular mechanisms by which they adapt to extreme (thermo/acidophilic) conditions, and this may lead to new green enzymatic catalysts and technologies for industry.

scholarly journals StrainPro – a highly accurate Metagenomic strain-level profiling tool

2019 ◽  
Author(s):  
Hsin-Nan Lin ◽  
Yaw-Ling Lin ◽  
Wen-Lian Hsu
Keyword(s):  
Microbial Community ◽  
Relative Abundance ◽  
Taxonomic Diversity ◽  
Evaluation Study ◽  
Taxonomic Composition ◽  
Strain Level ◽  
Metagenomic Analysis ◽  
Reference Database ◽  
Analysis Tool ◽  
Analysis Tools

ABSTRACTCharacterizing the taxonomic diversity of a microbial community is very important to understand the roles of microorganisms. Next generation sequencing (NGS) provides great potential for investigation of a microbial community and leads to Metagenomic studies. NGS generates DNA fragment sequences directly from microorganism samples, and it requires analysis tools to identify microbial species (or taxonomic composition) and estimate their relative abundance in the studied community. However, only a few tools could achieve strain-level identification and most tools estimate the microbial abundances simply according to the read counts. An evaluation study on metagenomic analysis tools concludes that the predicted abundance differed significantly from the true abundance. In this study, we present StrainPro, a novel metagenomic analysis tool which is highly accurate both at characterizing microorganisms at strain-level and estimating their relative abundances. A unique feature of StrainPro is it identifies representative sequence segments from reference genomes. We generate three simulated datasets using known strain sequences and another three simulated datasets using unknown strain sequences. We compare the performance of StrainPro with seven existing tools. The results show that StrainPro not only identifies metagenomes with high precision and recall, but it is also highly robust even when the metagenomes are not included in the reference database. Moreover, StrainPro estimates the relative abundance with high accuracy. We demonstrate that there is a strong positive linear relationship between observed and predicted abundances.

scholarly journals Temporal and spatial dynamics of peat microbiomes in drained and rewetted soils of three temperate peatlands

2020 ◽  
Author(s):  
Haitao Wang ◽  
Micha Weil ◽  
Dominik Zak ◽  
Diana Münch ◽  
Anke Günther ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Greenhouse Gas Emissions ◽  
Greenhouse Gas ◽  
Community Composition ◽  
Structural Equation ◽  
Structural Equation Models ◽  
Temporal Dynamics ◽  
Salt Water ◽  
Microbial Community Composition ◽  
Gas Emissions

AbstractBackgroundDrainage of high-organic peatlands for agricultural purposes has led to increased greenhouse gas emissions and loss of biodiversity. In the last decades, rewetting of peatlands is on the rise worldwide, to mitigate these negative impacts. However, it remains still questionable how rewetting would influence peat microbiota as important drivers of nutrient cycles and ecosystem restoration. Here, we investigate the spatial and temporal dynamics of the diversity, community composition and network interactions of prokaryotes and eukaryotes, and the influence of rewetting on these microbial features in formerly long-term drained and agriculturally used fens. Peat-soils were sampled seasonally from three drained and three rewetted sites representing the dominating fen peatland types of glacial landscapes in Northern Germany, namely alder forest, costal fen and percolation fen.ResultsCostal fens as salt-water impacted systems showed a lower microbial diversity and their microbial community composition showed the strongest distinction from the other two peatland types. Prokaryotic and eukaryotic community compositions showed a congruent pattern which was mostly driven by peatland type and rewetting. Rewetting decreased the abundances of fungi and prokaryotic decomposers, while the abundance of potential methanogens was significantly higher in the rewetted sites. Rewetting also influenced the abundance of ecological clusters in the microbial communities identified from the co-occurrence network. The microbial communities changed only slightly with depth and over time. According to structural equation models rewetted conditions affected the microbial communities through different mechanisms across the three studied peatland types.ConclusionsOur results suggest that rewetting strongly impacts the structure of microbial communities and, thus, important biogeochemical processes, which may explain the high variation in greenhouse gas emissions upon rewetting of peatlands. The improved understanding of functional mechanisms of rewetting in different peatland types lays the foundation for securing best practices to fulfil multiple restoration goals including those targeting on climate, water, and species protection.

scholarly journals PSI-10 Establishing a foundation to harvest the potential of the microbiome in poultry production

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 293-294
Author(s):  
Camila S Marcolla ◽  
Benjamin Willing
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Community Composition ◽  
Relative Abundance ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Poultry Production ◽  
Microbiota Composition ◽  
Microbial Composition ◽  
The Impact

Abstract This study aimed to characterize poultry microbiota composition in commercial farms using 16S rRNA sequencing. Animals raised in sanitized environments have lower survival rates when facing pathogenic challenges compared to animals naturally exposed to commensal organisms. We hypothesized that intensive rearing practices inadvertently impair chicken exposure to microbes and the establishment of a balanced gut microbiota. We compared gut microbiota composition of broilers (n = 78) and layers (n = 20) from different systems, including commercial intensive farms with and without in-feed antibiotics, organic free-range farms, backyard-raised chickens and chickens in an experimental farm. Microbial community composition of conventionally raised broilers was significantly different from antibiotic-free broilers (P = 0.012), from broilers raised outdoors (P = 0.048) and in an experimental farm (P = 0.006) (Fig1). Significant community composition differences were observed between antibiotic-fed and antibiotic-free chickens (Fig2). Antibiotic-free chickens presented higher alpha-diversity, higher relative abundance of Deferribacteres, Fusobacteria, Bacteroidetes and Actinobacteria, and lower relative abundance of Firmicutes, Clostridiales and Enterobacteriales than antibiotic-fed chickens (P < 0.001) (Fig3). Microbial community composition significantly changed as birds aged. In experimental farm, microbial community composition was significant different for 7, 21 and 35 day old broilers (P < 0.001), and alpha diversity increased from 7 to 21d (P < 0.024), but not from 21 to 35d; whereas, in organic systems, increases in alpha-diversity were observed from 7d to 21d, and from 21d to 35d (P < 0.05). Broilers and layers raised together showed no differences in microbiota composition and alpha diversity (P > 0.8). It is concluded that production practices consistently impact microbial composition, and that antibiotics significantly reduces microbial diversity. We are now exploring the impact of differential colonization in a controlled setting, to determine the impact of the microbes associated with extensively raised chickens. This study will support future research and the development of methods to isolate and introduce beneficial microbes to commercial systems.

scholarly journals Changes in microbial community composition, activity, and greenhouse gas production upon inundation of drained iron-rich peat soils

2020 ◽  
Vol 149 ◽  
pp. 107862
Author(s):  
Anniek E.E. de Jong ◽  
Simon Guererro-Cruz ◽  
Josepha M.H. van Diggelen ◽  
Annika Vaksmaa ◽  
Leon P.M. Lamers ◽  
...  
Keyword(s):  
Microbial Community ◽  
Greenhouse Gas ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Gas Production ◽  
Peat Soils

scholarly journals Dynamic hydrology and plant-mediated effects reduce greenhouse gas emissions and alter wetland microbial communities

2020 ◽  
Author(s):  
Regina B. Bledsoe ◽  
Ariane L. Peralta
Keyword(s):  
Microbial Community ◽  
Greenhouse Gas Emissions ◽  
Greenhouse Gas ◽  
Redox Status ◽  
Gas Production ◽  
Redox Conditions ◽  
Gas Emissions ◽  
Soil Redox ◽  
Microbial Function ◽  
Mediated Effects

AbstractWhile wetlands represent a small fraction (~7%) of the world’s land surface, it is estimated that one third of wetlands have been lost due to human activities. Wetland habitat loss decreases ecosystem functions such as improving water quality and mitigating climate change. These microbially mediated functions are dependent on particular soil redox conditions, which are altered by soil hydrology and the presence of plants. Differences in microbial physiology allow certain taxa (aerobes and facultative anaerobes) to adapt to fluctuating (dry/wet) hydrologic conditions, while other taxa (obligate anaerobes) are better adapted to continually saturated conditions. Therefore, the duration of hydrologic periods can affect soil microbial community structure and function. Further, plant-derived carbon, nutrients, and air are released by diffusion belowground which also impacts microbial activity in soils. In this study, we hypothesized that redox status due to continuous flooding would support greater abundance of microbial taxa involved in methanogenesis (obligate anaerobes), but plant-mediated oxygen transport would decrease methane emissions. Using a mesocosm design, we manipulated duration of hydrologic condition (i.e., stable dry, stable flooding, and alternating wet/dry) and presence of plants to induce soil redox changes in wetland soils. We measured soil redox status, used targeted amplicon sequencing to characterize the bacterial and archaeal communities, and measured greenhouse gas production to assess microbial function. Hydrology and to a lesser degree plant presence influenced soil redox conditions. Hydrologic history strongly influenced microbial community composition, but plant presence and hydrologic treatment altered microbial function to a great degree. As predicted, plant presence decreased greenhouse gas production in the wetland mesocosms. While previous studies do not often include plants when assessing greenhouse gas emissions, this study highlights that plant-mediated decreases in greenhouse gas emissions are significant. If plant-mediated effects are not considered when estimating the carbon balance of ecosystems, then wetland carbon storage could be underestimated.

scholarly journals Degradation of recalcitrant polyurethane and xenobiotic additives by a selected landfill microbial community and its biodegradative potential revealed by proximity ligation-based metagenomic analysis

2019 ◽  
Author(s):  
Itzel Gaytán ◽  
Ayixon Sánchez-Reyes ◽  
Manuel Burelo ◽  
Martín Vargas-Suárez ◽  
Ivan Liachko ◽  
...  
Keyword(s):  
Microbial Community ◽  
Metagenomic Analysis ◽  
Contaminated Sites ◽  
Physical Analysis ◽  
Glycol Ethers ◽  
Metabolic Potential ◽  
Proximity Ligation ◽  
Polyurethane Acrylate ◽  
Biodegradation Process ◽  
Genes Encoding

ABSTRACTPolyurethanes (PU) are the sixth more produced plastics with around 19-million tons/year, but since they are not recyclable they are burned or landfilled, generating ecological damage. To elucidate the mechanisms that landfill microbial communities perform to attack recalcitrant PU plastic, we studied the BP8 community selected by its capability to grow in a water PU dispersion (WPUD) that contains a polyether-polyurethane-acrylate (PE-PU-A) copolymer and xenobiotic additives (N-methyl 2-pyrrolidone, isopropanol and glycol ethers), and performed a proximity ligation-based metagenomic analysis for revealing the community structure and potential biodegradative capacity. Additives were consumed early whereas the copolymer was cleaved throughout the 25-days incubation. BP8 metagenomic deconvolution reconstructed five genomes, three of them from novel species. Genes encoding enzymes for additives biodegradation were predicted. The chemical and physical analysis of the biodegradation process, and the identified biodegradation products show that BP8 cleaves esters, aromatic urethanes, C-C and ether groups by hydrolytic and oxidative mechanisms. The metagenomic analysis allowed to predicting comprehensive metabolic pathways and enzymes that explain the observed PU biodegradation. This is the first study revealing the metabolic potential of a landfill microbial community that thrives within a WPUD system and shows potential for bioremediation of polyurethane- and xenobiotic additives-contaminated sites.

scholarly journals Map Reveals Hot Spots for Arctic Greenhouse Gas Emissions

Eos ◽  
2016 ◽  
Vol 97 ◽  
Author(s):  
JoAnna Wendel
Keyword(s):  
Greenhouse Gas Emissions ◽  
Greenhouse Gas ◽  
Hot Spots ◽  
Gas Emissions ◽  
Arctic Conditions

By bringing together data on permafrost stability, soils, and other Arctic conditions, scientists have plotted where permafrost is vulnerable to collapse, which could release long-stored carbon.

scholarly journals Changes in Microbial Community Phylogeny and Metabolic Activity Along the Water Column Uncouple at Near Sediment Aphotic Layers in Fjords

2021 ◽  
Author(s):  
Sven P. Tobias-Hünefeldt ◽  
Stephen R. Wing ◽  
Federico Baltar ◽  
Sergio E. Morales
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Water Column ◽  
Microbial Activity ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Leucine Incorporation ◽  
Metabolic Potential ◽  
Near Surface ◽  
Potential Activity

Abstract Fjords are semi-enclosed marine systems with unique physical conditions that influence microbial community composition and structure. Pronounced organic matter and physical condition gradients within fjords provide a natural laboratory for the study of changes in microbial phylogeny and metabolic potential in response to environmental conditions. Photosynthetic production in euphotic zones sustains deeper aphotic microbial activity via organic matter sinking, augmented by large terrestrial inputs. We profiled microbial functional potential (Biolog Ecoplates), bacterial abundance, heterotrophic production (3H-Leucine incorporation), and prokaryotic/eukaryotic community composition (16S and 18S rRNA amplicon gene sequencing) to link metabolic potential, activity, and community composition to known community drivers. Similar factors shaped metabolic potential, activity and community (prokaryotic and eukaryotic) composition across surface/near surface sites. However, increased metabolic diversity at near bottom (aphotic) sites reflected an organic matter influence from sediments. Photosynthetically produced particulate organic matter shaped the upper water column community composition and metabolic potential. In contrast, microbial activity at deeper aphotic waters were strongly influenced by other organic matter imput than sinking marine snow (e.g. sediment resuspension of benthic organic matter, remineralisation of terrestrially derived organic matter, etc.), severing the link between phylogeny and metabolic potential. Taken together, different organic matter sources shape microbial activity, but not community composition, in New Zealand fjords.

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