Microbial activity and community structure in two drained fen soils in the Ljubljana Marsh

Kraigher, Barbara; Stres, Blaž; Hacin, Janez; Ausec, Luka; Mahne, Ivan; Elsas, Jan Dirk van; Mandić-Mulec, Ines

doi:10.1016/j.soilbio.2006.04.031

Cited by 65 publications

(58 citation statements)

References 31 publications

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“…S2 in the supplemental material). Most of the detected bacterial 16S rRNA gene sequences were affiliated with the phyla Proteobacteria and Acidobacteria ( Table 3), taxa that have been observed to be dominant in other boggy soils (15,40,43). The detection of the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes, Spirochaetes, and Verrucomicrobia is likewise consistent with the occurrence of these taxa in other fens and bogs (15,40,43).…”

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confidence: 69%

“…Several studies have demonstrated that wetland soils contain complex prokaryotic communities (10,15,40,43), a finding consistent with the aforementioned network of trophically linked processes that yield methane. The methanogenic community of the fen Schlöppnerbrunnen in southeast Germany is composed of Methanobacteriaceae, Methanomicrobiaceae, Methanosaetaceae, and Methanosarcinaceae (32,90).…”

supporting

confidence: 66%

“…Most of the detected bacterial 16S rRNA gene sequences were affiliated with the phyla Proteobacteria and Acidobacteria ( Table 3), taxa that have been observed to be dominant in other boggy soils (15,40,43). The detection of the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes, Spirochaetes, and Verrucomicrobia is likewise consistent with the occurrence of these taxa in other fens and bogs (15,40,43). Previous studies have documented the occurrence of Crenarchaeota in the fen Schlöppnerbrunnen (32,90), and half of the detected archaeal 16S rRNA phylotypes were affiliated with this phylum ( Table 2).…”

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confidence: 99%

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Competing Formate- and Carbon Dioxide-Utilizing Prokaryotes in an Anoxic Methane-Emitting Fen Soil

Hunger

Schmidt

Hilgarth

et al. 2011

Appl Environ Microbiol

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Methanogenesis in wetlands is dependent on intermediary substrates derived from the degradation of biopolymers. Formate is one such substrate and is stimulatory to methanogenesis and acetogenesis in anoxic microcosms of soil from the fen Schlöppnerbrunnen. Formate dissimilation also yields CO 2 as a potential secondary substrate. The objective of this study was to resolve potential differences between anaerobic formateand CO 2 -utilizing prokaryotes of this fen by stable isotope probing. Anoxic soil microcosms were pulsed daily with low concentrations of 13 C]formate treatments, but labeling of known acetogenic taxa was not detected. However, several phylotypes were affiliated with acetogen-containing taxa (e.g., Sporomusa). Methanosaetaceae-affiliated methanogens appeared to participate in the consumption of acetate. Twelve and 58 family-level archaeal and bacterial 16S rRNA phylotypes, respectively, were detected, approximately half of which had no isolated representatives. Crenarchaeota constituted half of the detected archaeal 16S rRNA phylotypes. The results highlight the unresolved microbial diversity of the fen Schlöppnerbrunnen, suggest that differing taxa competed for the same substrate, and indicate that Methanocellaceae, Methanobacteriaceae, Methanosarcinaceae, and Methanosaetaceae were linked to the production of methane, but they do not clearly resolve the taxa responsible for the apparent conversion of formate to acetate.

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confidence: 69%

supporting

confidence: 66%

Section: Downloaded Frommentioning

confidence: 99%

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Competing Formate- and Carbon Dioxide-Utilizing Prokaryotes in an Anoxic Methane-Emitting Fen Soil

Hunger

Schmidt

Hilgarth

et al. 2011

Appl Environ Microbiol

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“…The main groups of clones found from a Sphagnum-dominated peatland in Siberia were affiliated with the phyla Acidobacteria, Alphaproteobacteria, Verrucomicrobia, Actinobacteria, Deltaproteobacteria, Chloroflexi and Planctomycetes (Dedysh et al 2006). The majority of bacterial clones from two drained fen sites in Slovenia consisted of Acidobacteria (23%), Alpha-(16%), Beta-(12%), Gamma-(8%) and Deltaproteobacteria (17%), Planctomycetes (7%) and Actinobacteria (6%) (Kraigher et al 2006). In addition, bacterial clones from Sphagnum-dominated peatlands in NE USA (New England) were dominated by Proteobacteria (54%), Firmicutes and Acidobacteria (11%), and the rest of the clones were similar to Verrucomicrobia, Actinobacteria and Planctomycetes (Morales et al 2006).…”

Section: Bacteriamentioning

confidence: 99%

Aerobic carbon-cycle related microbial communities in boreal peatlands: responses to water-level drawdown

Peltoniemi¹

2010

Diss. For.

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Boreal peatlands represent a considerable portion of the global carbon (C) pool. These environments are vulnerable to changes in water level (WL), which can vary dramatically in response to climate or land-use change. Water-level drawdown (WLD) causes peatland drying and induces a vegetation change, which in turn affects the decomposition of soil organic matter and the release of greenhouse gases (CO 2 and CH 4 ) into the atmosphere. The objective of this thesis was to study the microbial communities related to the C cycle and their response to WLD in two boreal peatlands.The first study site (Lakkasuo) is a boreal peatland complex that was partly drained in 1961 to investigate the long-term effects of WLD, and includes three site types with different nutrient levels. At the same location, an experiment simulating the predicted effect of climate change was carried out in 2001 to study the short-term effects of WLD. The second study site (Suonukkasuo) is a boreal fen with a WL gradient caused by a groundwater extraction plant; the undisturbed fen grades into a pine-dominated peatland forest. Microbial communities were studied with phospholipid fatty acid (PLFA) analysis, PCR-DGGE and multivariate analysis.Both sampling depth and site type had a strong impact on all microbial communities. In general, bacteria dominated the deeper layers of the nutrient-rich fen and the wettest surfaces of the nutrient-poor bog sites, whereas fungi seemed more abundant in the drier surfaces of the nutrient-poor bog. WLD clearly affected the microbial communities but the effect was dependent on site type. Fungi and Gram-negative bacteria seemed to benefit and actinobacteria to suffer from the WLD in the fens. The fungal and methane-oxidizing bacteria (MOB) community composition changed at all sites but the actinobacterial community response was apparent only in the nutrientrich fen after WLD.The actinobacterial response to WLD was minor compared to that of the fungal community. The response was greatest in the nutrient-rich fen and least in the nutrient-poor bog. Microbial communities became more similar among sites after long-term WLD. Litter quality had a large impact on community composition, whereas the effects of site type and WLD were relatively minor. The decomposition rate of fresh organic matter was influenced slightly by actinobacteria, but not at all by fungi. Overall, the results were in line with patterns of vegetation change in the study sites.Field respiration measurements in the northern fen indicated that short term WLD accelerates the decomposition of soil organic matter. In addition, a correlation between activity and certain fungal sequences indicated that community composition affects the decomposition of old organic matter in deeper layers of the peat profile. Fungal sequences were matched to taxa capable of utilizing a broad range of substrates. Most of the actinobacterial sequences could not be matched to characterized taxa in reference databases. WLD had a negative impact on CH 4 oxidation, especiall...

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“…The results are understandable in that many Proteobacterial members such as Bradyrhizobium spp. in soil are considered "fast users" of readily available carbonaceous substrates, and can metabolize a variety of substrates (7). Sequences for the spots excised from the activated sludge 2-DGE maps were also largely identical.…”

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confidence: 91%

Analysis of Bacterial Populations in the Environment Using Two-dimensional Gel Electrophoresis of Genomic DNA and Complementary DNA

et al. 2011

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Two-dimensional gel electrophoresis (2-DGE) mapping of genomic DNA and complementary DNA (cDNA) amplicons was attempted to analyze total and active bacterial populations within soil and activated sludge samples. Distinct differences in the number and species of bacterial populations and those that were metabolically active at the time of sampling were visually observed especially for the soil community. Statistical analyses and sequencing based on the 2-DGE data further revealed the relationships between total and active bacterial populations within each community. This high-resolution technique would be useful for obtaining a better understanding of bacterial population structures in the environment.Key words: 2-DGE mapping, 16S rRNA gene, total and active bacterial populations, soil, activated sludge Over the last decade, the polymerase chain reaction (PCR) targeting the 16S ribosomal RNA (rRNA) gene has been widely applied to the study of bacterial communities in complex environmental systems such as soil (6, 13). In general, genomic DNA is extracted from environmental samples and purified. PCR is used to produce a large number of DNA fragments with universal primers for the 16S rRNA gene (rDNA) (9). These fragments obtained by the amplification are then subjected to molecular analyses that could provide insights into the major bacterial populations within a community. In addition, the direct isolation of ribosome RNA from an environmental sample, followed by reverse transcription (RT)-PCR and molecular profiling, enables the assessment of metabolically active members, as the amount of rRNA in cells can be correlated to cellular activity (8,14) or may reflect a rough estimate of the bacterial growth rate (18).A two-dimensional DNA gel electrophoresis (2-DGE) mapping technique was developed to separate PCR amplicons with high resolution (5, 10). Due to the increase in resolution, the 2-DGE mapping would be a useful molecular tool for assessing bacterial communities in environments. In the present paper, we aimed to compare bacterial DNAand cDNA-based 2-DGE maps from environmental samples such as soil and activated sludge.Total soil DNA and RNA were isolated from a forest soil sample (0.5 g) collected from the campus of Yokohama National University, Japan using an ISOIL for beads beating DNA extraction kit (Nippon Gene, Toyama, Japan) and a FastRNA Pro soil direct kit (Qbiogene, Carlsbad, USA) according to the manufacturer's instructions, respectively. Total bacterial DNA and RNA for an aqueous activated sludge sample (1 mL), obtained from a municipal wastewater treatment plant in Yokohama, Japan, were simultaneously extracted using TRI reagent (Cosmo Bio, Tokyo, Japan) according to the protocol provided by Molecular Research Center (Cincinnati, USA).The extracted DNA was purified using two spin columns as described previously (10). The RNA aliquots were treated with a Deoxyribonuclease treatment kit (RT grade, Nippon Gene). Single-stranded cDNA was synthesized by a RT reaction of total RNA using random prime...

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Microbial activity and community structure in two drained fen soils in the Ljubljana Marsh

Cited by 65 publications

References 31 publications

Competing Formate- and Carbon Dioxide-Utilizing Prokaryotes in an Anoxic Methane-Emitting Fen Soil

Competing Formate- and Carbon Dioxide-Utilizing Prokaryotes in an Anoxic Methane-Emitting Fen Soil

Aerobic carbon-cycle related microbial communities in boreal peatlands: responses to water-level drawdown

Analysis of Bacterial Populations in the Environment Using Two-dimensional Gel Electrophoresis of Genomic DNA and Complementary DNA

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