scholarly journals Dead bacterial biomass-assimilating bacterial populations in compost revealed by high-sensitivity stable isotope probing

2019 ◽  
Vol 133 ◽  
pp. 105235
Author(s):  
Dai Hanajima ◽  
Tomo Aoyagi ◽  
Tomoyuki Hori
Keyword(s):  
Stable Isotope ◽  
Bacterial Biomass ◽  
High Sensitivity ◽  
Stable Isotope Probing ◽  
Bacterial Populations

scholarly journals Subgroup level differences of physiological activities in marine Lokiarchaeota

2020 ◽  
Author(s):  
Xiuran Yin ◽  
Mingwei Cai ◽  
Yang Liu ◽  
Guowei Zhou ◽  
Tim Richter-Heitmann ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Marine Sediments ◽  
Inorganic Carbon ◽  
Bacterial Biomass ◽  
Stable Isotope Probing ◽  
Aromatic Compound Degradation ◽  
Lactate Degradation ◽  
Globally Distributed ◽  
Mud Area

Abstract Asgard is a recently discovered archaeal superphylum, closely linked to the emergence of eukaryotes. Among Asgard archaea, Lokiarchaeota are abundant in marine sediments, but their in situ activities are largely unknown except for Candidatus ‘Prometheoarchaeum syntrophicum’. Here, we tracked the activity of Lokiarchaeota in incubations with Helgoland mud area sediments (North Sea) by stable isotope probing (SIP) with organic polymers, 13C-labelled inorganic carbon, fermentation intermediates and proteins. Within the active archaea, we detected members of the Lokiarchaeota class Loki-3, which appeared to mixotrophically participate in the degradation of lignin and humic acids while assimilating CO2, or heterotrophically used lactate. In contrast, members of the Lokiarchaeota class Loki-2 utilized protein and inorganic carbon, and degraded bacterial biomass formed in incubations. Metagenomic analysis revealed pathways for lactate degradation, and involvement in aromatic compound degradation in Loki-3, while the less globally distributed Loki-2 instead rely on protein degradation. We conclude that Lokiarchaeotal subgroups vary in their metabolic capabilities despite overlaps in their genomic equipment, and suggest that these subgroups occupy different ecologic niches in marine sediments.

scholarly journals Nutrient Amendments in Soil DNA Stable Isotope Probing Experiments Reduce the Observed Methanotroph Diversity

2006 ◽  
Vol 73 (3) ◽  
pp. 798-807 ◽  
Author(s):  
Aur�lie C�bron ◽  
Levente Bodrossy ◽  
Nancy Stralis-Pavese ◽  
Andrew C. Singer ◽  
Ian P. Thompson ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Stable Isotope Probing ◽  
Population Diversity ◽  
Type I ◽  
Mineral Salts ◽  
Bacterial Populations ◽  
Soil Dna ◽  
Gradient Gel Electrophoresis ◽  
Soil Water Conditions

ABSTRACT Stable isotope probing (SIP) can be used to analyze the active bacterial populations involved in a process by incorporating 13C-labeled substrate into cellular components such as DNA. Relatively long incubation times are often used with laboratory microcosms in order to incorporate sufficient 13C into the DNA of the target organisms. Addition of nutrients can be used to accelerate the processes. However, unnatural concentrations of nutrients may artificially change bacterial diversity and activity. In this study, methanotroph activity and diversity in soil was examined during the consumption of 13CH4 with three DNA-SIP experiments, using microcosms with natural field soil water conditions, the addition of water, and the addition of mineral salts solution. Methanotroph population diversity was studied by targeting 16S rRNA and pmoA genes. Clone library analyses, denaturing gradient gel electrophoresis fingerprinting, and pmoA microarray hybridization analyses were carried out. Most methanotroph diversity (type I and type II methanotrophs) was observed in nonamended SIP microcosms. Although this treatment probably best reflected the in situ environmental conditions, one major disadvantage of this incubation was that the incorporation of 13CH4 was slow and some cross-feeding of 13C occurred, thereby leading to labeling of nonmethanotroph microorganisms. Conversely, microcosms supplemented with mineral salts medium exhibited rapid consumption of 13CH4, resulting in the labeling of a less diverse population of only type I methanotrophs. DNA-SIP incubations using water-amended microcosms yielded faster incorporation of 13C into active methanotrophs while avoiding the cross-feeding of 13C.

scholarly journals Identification of Acetate-Assimilating Microorganisms under Methanogenic Conditions in Anoxic Rice Field Soil by Comparative Stable Isotope Probing of RNA

2006 ◽  
Vol 73 (1) ◽  
pp. 101-109 ◽  
Author(s):  
Tomoyuki Hori ◽  
Matthias Noll ◽  
Yasuo Igarashi ◽  
Michael W. Friedrich ◽  
Ralf Conrad
Keyword(s):  
Stable Isotope ◽  
Rice Field ◽  
Ferric Iron ◽  
Stable Isotope Probing ◽  
Polymorphism Analysis ◽  
Field Soil ◽  
Bacterial Populations ◽  
Density Fractions ◽  
Reverse Transcription Pcr ◽  
Rice Field Soil

ABSTRACT Acetate is the most abundant intermediate of organic matter degradation in anoxic rice field soil and is converted to CH4 and/or CO2. Aceticlastic methanogens are the primary microorganisms dissimilating acetate in the absence of sulfate and reducible ferric iron. In contrast, very little is known about bacteria capable of assimilating acetate under methanogenic conditions. Here, we identified active acetate-assimilating microorganisms by using a combined approach of frequent label application at a low concentration and comparative RNA-stable isotope probing with 13C-labeled and unlabeled acetate. Rice field soil was incubated anaerobically at 25°C for 12 days, during which 13C-labeled acetate was added at a concentration of 500 μM every 3 days. 13C-labeled CH4 and CO2 were produced from the beginning of the incubation and accounted for about 60% of the supplied acetate 13C. RNA was extracted from the cells in each sample taken and separated by isopycnic centrifugation according to molecular weight. Bacterial and archaeal populations in each density fraction were screened by reverse transcription-PCR-mediated terminal restriction fragment polymorphism analysis. No differences in the bacterial populations were observed throughout the density fractions of the unlabeled treatment. However, in the heavy fractions of the 13C treatment, terminal restriction fragments (T-RFs) of 161 bp and 129 bp in length predominated. These T-RFs were identified by cloning and sequencing of 16S rRNA as from a Geobacter sp. and an Anaeromyxobacter sp., respectively. Apparently these bacteria, which are known as dissimilatory iron reducers, were able to assimilate acetate under methanogenic conditions, i.e., when CO2 was the predominant electron acceptor. We hypothesize that ferric iron minerals with low bioavailability might have served as electron acceptors for Geobacter spp. and Anaeromyxobacter spp. under these conditions.

scholarly journals Active viral population dynamics in frozen Arctic peat soil revealed with H218O stable isotope probing metagenomics

2021 ◽  
Author(s):  
Gareth Trubl ◽  
Jeffrey A. Kimbrel ◽  
Jose Liquet-Gonzalez ◽  
Erin E. Nuccio ◽  
Peter K. Weber ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Peat Soil ◽  
Stable Isotope Probing ◽  
Viral Population ◽  
Soil Processes ◽  
Carbohydrate Utilization ◽  
Bacterial Populations ◽  
Viral Ecology ◽  
Bacterial Phyla ◽  
Winter Conditions

AbstractWinter soil processes are critical to the carbon balance of northern ecosystems, yet the microbial ecology governing biogeochemical cycling in frozen soils is largely unknown. We used stable isotope probing targeted metagenomics to reveal the genomic potential of active microbial populations, with an emphasis on viruses, in soils. Peat soils were incubated under simulated winter conditions (subzero and anoxic) with H218O or natural abundance water for 184 and 370 days. Isotope incorporation revealed 46 active bacterial populations (MAGs; spanning 9 bacterial phyla) and 243 active viral populations (vOTUs). Active hosts were predicted for 33% of the active vOTUs and were some of the most abundant MAGs, having capacity for fermentation and carbohydrate utilization. Additionally, almost one-third of vOTUs carried auxiliary metabolic genes spanning five functional categories, highlighting the potential impact of viruses in microbial biogeochemistry. CO2 production throughout the incubation supports our evidence of microbial activities under winter conditions. Our results revealed a multi-trophic and changing microbial community in tandem with a changing viral community targeting dominant active bacteria consistent with the “kill-the-winner” hypothesis. These data have important implications for low-temperature soil processes in northern peatlands and reveal active host-linked soil viral ecology, with potential multifaceted biogeochemical impacts.

scholarly journals Characterization of growing bacterial populations in McMurdo Dry Valley soils through stable isotope probing with18O-water

2014 ◽  
Vol 89 (2) ◽  
pp. 415-425 ◽  
Author(s):  
Egbert Schwartz ◽  
David J. Van Horn ◽  
Heather N. Buelow ◽  
Jordan G. Okie ◽  
Michael N. Gooseff ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Stable Isotope Probing ◽  
Bacterial Populations ◽  
Dry Valley

scholarly journals Identification of active and taxonomically diverse 1,4-dioxane degraders in a full-scale activated sludge system by high-sensitivity stable isotope probing

2018 ◽  
Vol 12 (10) ◽  
pp. 2376-2388 ◽  
Author(s):  
Tomo Aoyagi ◽  
Fumiaki Morishita ◽  
Yutaka Sugiyama ◽  
Daisuke Ichikawa ◽  
Daisuke Mayumi ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Activated Sludge ◽  
High Sensitivity ◽  
Stable Isotope Probing ◽  
Full Scale ◽  
Activated Sludge System

scholarly journals Diversity of Anaerobic Microorganisms Involved in Long-Chain Fatty Acid Degradation in Methanogenic Sludges as Revealed by RNA-Based Stable Isotope Probing

2007 ◽  
Vol 73 (13) ◽  
pp. 4119-4127 ◽  
Author(s):  
Masashi Hatamoto ◽  
Hiroyuki Imachi ◽  
Yuto Yashiro ◽  
Akiyoshi Ohashi ◽  
Hideki Harada
Keyword(s):  
Fatty Acid ◽  
Stable Isotope ◽  
Major Fatty Acid ◽  
Stable Isotope Probing ◽  
Chain Fatty Acid ◽  
Long Chain Fatty Acid ◽  
Bacterial Populations ◽  
Anaerobic Microorganisms ◽  
Degrading Bacteria ◽  
Long Chain

ABSTRACT Long-chain fatty acid (LCFA) degradation is a key step in methanogenic treatment of wastes/wastewaters containing high concentrations of lipids. However, despite the importance of LCFA-degrading bacteria, their natural diversity is little explored due to the limited availability of isolate information and the lack of appropriate molecular markers. We therefore investigated these microbes by using RNA-based stable isotope probing. We incubated four methanogenic sludges (mesophilic sludges MP and MBF and thermophilic sludges TP and JET) with 13C-labeled palmitate (1 mM) as a substrate. After 8 to 19 days of incubation, we could detect 13C-labeled bacterial rRNA. A density-resolved terminal restriction fragment length polymorphism fingerprinting analysis showed distinct bacterial populations in 13C-labeled and unlabeled rRNA fractions. The bacterial populations in the 13C-labeled rRNA fractions were identified by cloning and sequencing of reverse-transcribed 16S rRNA. Diverse phylogenetic bacterial sequences were retrieved, including those of members of the family Syntrophaceae, clone cluster MST belonging to the class Deltaproteobacteria, Clostridium clusters III and IV, phylum Bacteroidetes, phylum Spirochaetes, and family Syntrophomonadaceae. Although Syntrophomonadaceae species are considered to be the major fatty acid-degrading syntrophic microorganisms under methanogenic conditions, they were detected in only two of the clone libraries. These results suggest that phylogenetically diverse bacterial groups were active in situ in the degradation of LCFA under methanogenic conditions.

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