81 research outputs found
CO2 conversion to methane and biomass in obligate methylotrophic methanogens in marine sediments
No full textMethyl substrates are important compounds for methanogenesis in marine sediments but diversity and carbon utilization by methylotrophic methanogenic archaea have not been clarified. Here, we demonstrate that RNA-stable isotope probing (SIP) requires C-13-labeled bicarbonate as co-substrate for identification of methylotrophic methanogens in sediment samples of the Helgoland mud area, North Sea. Using lipid-SIP, we found that methylotrophic methanogens incorporate 60-86% of dissolved inorganic carbon (DIC) into lipids, and thus considerably more than what can be predicted from known metabolic pathways (similar to 40% contribution). In slurry experiments amended with the marine methylotroph Methanococcoides methylutens, up to 12% of methane was produced from CO2, indicating that CO2-dependent methanogenesis is an alternative methanogenic pathway and suggesting that obligate methylotrophic methanogens grow in fact mixotrophically on methyl compounds and DIC. Although methane formation from methanol is the primary pathway of methanogenesis, the observed high DIC incorporation into lipids is likely linked to CO2-dependent methanogenesis, which was triggered when methane production rates were low. Since methylotrophic methanogenesis rates are much lower in marine sediments than under optimal conditions in pure culture, CO2 conversion to methane is an important but previously overlooked methanogenic process in sediments for methylotrophic methanogens
Manganese reduction and associated microbial communities in Antarctic surface sediments
No full textThe polar regions are the fastest warming places on earth. Accelerated glacial melting causes increased supply of nutrients such as metal oxides (i.e., iron and manganese oxides) into the surrounding environment, such as the marine sediments of Potter Cove, King George Island/Isla 25 de Mayo (West Antarctic Peninsula). Microbial manganese oxide reduction and the associated microbial communities are poorly understood in Antarctic sediments. Here, we investigated this process by geochemical measurements of in situ sediment pore water and by slurry incubation experiments which were accompanied by 16S rRNA sequencing. Members of the genus Desulfuromusa were the main responder to manganese oxide and acetate amendment in the incubations. Other organisms identified in relation to manganese and/or acetate utilization included Desulfuromonas, Sva1033 (family of Desulfuromonadales) and unclassified Arcobacteraceae. Our data show that distinct members of Desulfuromonadales are most active in organotrophic manganese reduction, thus providing strong evidence of their relevance in manganese reduction in permanently cold Antarctic sediments.Fil: Wunder, Lea C.. Universitat Bremen; AlemaniaFil: Breuer, Inga. Universitat Bremen; AlemaniaFil: Willis Poratti, Graciana. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universitat Bremen; AlemaniaFil: Aromokeye, David A.. Universitat Bremen; AlemaniaFil: Henkel, Susann. Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung; AlemaniaFil: Richter Heitmann, Tim. Universitat Bremen; AlemaniaFil: Yin, Xiuran. Universitat Bremen; AlemaniaFil: Friedrich, Michael W.. Universitat Bremen; Alemani
(Acido)bakterielle Diversität in Zeit und Raum
No full textRecent technological achievements enabled microbiologists to fully grasp the vast diversity of microbial life that is resident in soils, highly complex matrices of alternating micro-habitats on very small scales. Since then, microbial community composition has been catalogued for many different terrestrial habitats. This triggered the investigation and definition of processes which shape these communities. In most cases, the environment determines community composition, and similar habitats may feature similar microbial communities despite being far apart. However, some habitats have been described as subjected to pronounced neutral processes, which are dispersal, ecological drift or speciation. The balance between these process types is now the subject of many studies looking at microbial communities. It is also clear that these processes need to be monitored on both temporal and spatial scales, as the two dimensions are inseparably interlinked. However, most microbial studies deal with only one aspect, but do not control for the other. In this work, the outcome of a highly sophisticated plot scale experiment is presented encompassing 358 sampling locations distributed between six intra-annual sampling points on a 10 m x 10 m unfertilized grassland site in the Swabian Alb. RNA was extracted from the A-horizon of each soil and the hypervariable region 3 of the ribosomal small subunit was amplified and sequenced with barcoded Illumina sequencing. Roughly 400 million eubacterial reads were obtained. The dataset was used to assess the population dynamics of Acidobacteria, as well as the spatio-temporal co-occurenze of functionally depending microorganism. Additionally, preliminary results motivated the assessment of common methods for the examination of rhizospheric communities. In combination, the diversity of bacterial communities in space and time was tested from different angles, reflecting different research question, and they all revealed a far more complex reality than previously thought
(Acido)bacterial diversity in space and time
No full textRecent technological achievements enabled microbiologists to fully grasp the vast diversity of microbial life that is resident in soils, highly complex matrices of alternating micro-habitats on very small scales. Since then, microbial community composition has been catalogued for many different terrestrial habitats. This triggered the investigation and definition of processes which shape these communities. In most cases, the environment determines community composition, and similar habitats may feature similar microbial communities despite being far apart. However, some habitats have been described as subjected to pronounced neutral processes, which are dispersal, ecological drift or speciation. The balance between these process types is now the subject of many studies looking at microbial communities. It is also clear that these processes need to be monitored on both temporal and spatial scales, as the two dimensions are inseparably interlinked. However, most microbial studies deal with only one aspect, but do not control for the other. In this work, the outcome of a highly sophisticated plot scale experiment is presented encompassing 358 sampling locations distributed between six intra-annual sampling points on a 10 m x 10 m unfertilized grassland site in the Swabian Alb. RNA was extracted from the A-horizon of each soil and the hypervariable region 3 of the ribosomal small subunit was amplified and sequenced with barcoded Illumina sequencing. Roughly 400 million eubacterial reads were obtained. The dataset was used to assess the population dynamics of Acidobacteria, as well as the spatio-temporal co-occurenze of functionally depending microorganism. Additionally, preliminary results motivated the assessment of common methods for the examination of rhizospheric communities. In combination, the diversity of bacterial communities in space and time was tested from different angles, reflecting different research question, and they all revealed a far more complex reality than previously thought
Pore water geochemistry of surface sediments around South Georgia (Annenkov Trough GeoB22054-2, Church Trough GeoB22031-1, Cumberland Bay GeoB22046-1, Drygalski Trough GeoB22015-1)
No full textThe permanently cold sediments of South Georgia were investigated in this study to identify the geochemical parameters that are linked to microbial community composition. To identify these parameters, pore water profiles of sulfate, sulfide, dissolved iron, ammonium, silicate, dissolved inorganic carbon, and phosphate were analysed. The results presented here were obtained during the RV METEOR M134 expedition (January - March, 2017) and contribute to our understanding of microbial community composition in surface sediments of South Georgia
Functional traits and spatio-temporal structure of a major group of soil protists (Rhizaria: Cercozoa) in a temperate grassland.
No full text© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fiore-Donno, A. M., Richter-Heitmann, T., Degrune, F., Dumack, K., Regan, K. M., Marhan, S., Boeddinghaus, R. S., Rillig, M. C., Friedrich, M. W., Kandeler, E., & Bonkowski, M. Functional traits and spatio-temporal structure of a major group of soil protists (Rhizaria: Cercozoa) in a temperate grassland. Frontiers in Microbiology, 10, (2019): 1332, doi:10.3389/fmicb.2019.01332.Soil protists are increasingly appreciated as essential components of soil foodwebs; however, there is a dearth of information on the factors structuring their communities. Here we investigate the importance of different biotic and abiotic factors as key drivers of spatial and seasonal distribution of protistan communities. We conducted an intensive survey of a 10 m2 grassland plot in Germany, focusing on a major group of protists, the Cercozoa. From 177 soil samples, collected from April to November, we obtained 694 Operational Taxonomy Units representing >6 million Illumina reads. All major cercozoan taxonomic and functional groups were present, dominated by the small flagellates of the Glissomonadida. We found evidence of environmental selection structuring the cercozoan communities both spatially and seasonally. Spatial analyses indicated that communities were correlated within a range of 3.5 m. Seasonal variations in the abundance of bacterivores and bacteria, followed by that of omnivores suggested a dynamic prey-predator succession. The most influential edaphic properties were moisture and clay content, which differentially affected each functional group. Our study is based on an intense sampling of protists at a small scale, thus providing a detailed description of the biodiversity of different taxa/functional groups and the ecological processes involved in shaping their distribution.This work was partly supported by the DFG Priority Program 1374 “Infrastructure-Biodiversity-Exploratories.” Funding to AMF-D and MB was provided by BO 1907/18-1; funding to EK, SM, KMR, and RSB was provided by KA 1590/8-2 and KA 1590/8-3; funding to FD and MCR was provided by the BiodivERsA grant “Digging Deeper.” We are grateful to the Swiss National Science Foundation Grant 316030 150817 for funding the MiSeq instrument at the University of Geneva (CH)
Pore-water data of three gravity cores in South Georgia sediments
No full textIn this study pore-water constituents from three sampling locations in permanently cold sediments north of South Georgia island have been investigated. The three gravity cores from Cumberland Bay (GeoB22043-1), Royal Trough (GeoB22039-2) and Church Trough (GeoB22032-1) were sampled during the RV METEOR cruise M134 in 2017. The dataset contains measurements of pore-water constituents such as sulfate, sulfide, dissolved iron, dissolved inorganic carbon and dissolved manganese profiles which are relevant to microbial community composition in the sediments
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