Bacterial succession along a sediment porewater gradient at Lake Neusiedl in Austria

Hoyningen-Huene, Avril Jean Elisabeth von; Schneider, Dominik; Fussmann, Dario; Reimer, Andreas; Arp, Gernot; Daniel, Rolf

doi:10.1038/s41597-019-0172-9

Cited by 23 publications

(13 citation statements)

References 51 publications

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“…Bioinformatic processing of 16S rRNA gene amplicons was carried out using the protocol for bacterial 16S rRNA community of water and sediments described by von Hoyningen-Huene et al (2019) with the following modification. The paired-end (PE) reads from the Illumina MiSeq sequencing were first quality checked using fastp ( Chen et al, 2018 ) with the quality phred score of 20 (−q 20), minimum read length of 200 (−l 200), base correction by overlap (−c), as well as 5′-end trimming (−5 4) and 3′-end trimming (−3 4).…”

Section: Methodsmentioning

confidence: 99%

A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments

Huang

Yan

et al. 2021

Front. Microbiol.

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Molecular methods revealed that the majority of microbes in natural environments remains uncultivated. To fully understand the physiological and metabolic characteristics of microbes, however, culturing is still critical for microbial studies. Here, we used bacterial community analysis and four culture media, namely, traditional marine broth 2216 (MB), water extracted matter (WEM), methanol extracted matter (MEM), and starch casein agar (SCA), to investigate the diversity of cultivated bacteria in coastal sediments. A total of 1,036 isolates were obtained in pure culture, and they were classified into five groups, namely, Alphaproteobacteria (52.51%), Gammaproteobacteria (23.26%), Actinobacteria (13.32%), Firmicutes, and Bacteroidetes. Compared to other three media, WEM recovered a high diversity of actinobacteria (42 of 63 genotypes), with Micromonospora and Streptomyces as the most cultivated genera. Amplicon sequencing of the bacterial 16S ribosomal RNA (rRNA) gene V3–V4 fragment revealed eight dominant groups, Alphaproteobacteria (12.81%), Gammaproteobacteria (20.07%), Deltaproteobacteria (12.95%), Chloroflexi (13.09%), Bacteroidetes (8.28%), Actinobacteria (7.34%), Cyanobacteria (6.20%), and Acidobacteria (5.71%). The dominant members affiliated to Actinobacteria belonged to “Candidatus Actinomarinales,” “Candidatus Microtrichales,” and Nitriliruptorales. The cultivated actinobacteria accounted for a small proportion (<5%) compared to the actinobacterial community, which supported that the majority of actinobacteria are still waiting for cultivation. Our study concluded that WEM could be a useful and simple culture medium that enhanced the recovery of culturable actinobacteria from coastal sediments.

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Section: Methodsmentioning

confidence: 99%

A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments

Huang

Yan

et al. 2021

Front. Microbiol.

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“…The dataset with the most negative fitted slope is that for Daya Bay, China (Wu et al, 2021), where samples were collected from the surface, middle, and bottom of sediment cores. In addition, multiple lake and ocean datasets are characterized by higher Eh7 for overlying water than sediment (Han et al, 2019;von Hoyningen-Huene et al, 2019;Vavourakis et al, 2019;Molina et al, 2021); most of these exhibit negative correlations with Z C , except for Honghu Lake (Han et al, 2019), which shows a relatively high Z C for water. A systematic difference in redox potential between water and sediment is not evident for river datasets (Cai et al, 2019;Zárate et al, 2020).…”

Section: Sediment and Soilmentioning

confidence: 99%

“…The datasets with negative correlations represent marine (Sánchez-Soto Jiménez et al, 2018;Molina et al, 2021;Wu et al, 2021), coastal (Zhou et al, 2017), freshwater (Zárate et al, 2020;von Hoyningen-Huene et al, 2019), and hypersaline sediments (Vavourakis et al, 2019). The dataset with the most negative fitted slope is that for Daya Bay, China (Wu et al, 2021), where samples were collected from the surface, middle, and bottom of sediment cores.…”

Section: Sediment and Soilmentioning

confidence: 99%

Local and global chemical shaping of bacterial communities by redox potential

Dick

Meng

2021

Preprint

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Thermodynamics predicts a positive correlation between environmental redox potential and oxidation state of molecules; if found for microbial communities it would imply a new kind of deterministic eco-evolutionary process. This study examines evidence for local- and global-scale correlations between oxidation-reduction potential (ORP or Eh) in environmental samples and carbon oxidation state (ZC) of estimated bacterial and archaeal community proteomes. Seventy-nine public datasets for seven environment types (river & seawater, lake & pond, alkaline spring, hot spring, groundwater, sediment, and soil) were analyzed. Taxonomic abundances inferred from high-throughput 16S rRNA gene sequences were combined with NCBI Reference Sequence (RefSeq) proteomes to estimate the amino acid compositions and chemical formulas (CcHhNnOoSs) of community proteomes, which yield ZC. Alkaline hot springs have the lowest ZC for both bacterial and archaeal domains of any environment. Positive global correlations between redox potential and ZC are found for bacterial communities in lake & pond, groundwater, and soil environments, but not archaeal communities, suggesting a broad ecological signal of chemical shaping in Bacteria.

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“…While the concept that dolomite forms within sediments mediated by anaerobic microbial processes and their extracellular polymeric substances is widely acknowledged, another aspect should be taken into account: the site of dolomite formation may not always coincide with the location where the mineral is found due to relocation after precipitation. Several studies describe unlithified dolomite precipitation in warm, arid and hypersaline marine environments, like coastal sabkhas (Illing et al, 1965;Bontognali et al, 2010;Court et al, 2017), coastal lakes, such as Lagoa Vermelha in Brazil (Vasconcelos and McKenzie, 1997;van Lith et al, 2002;Sánchez-Román et al, 2009), and ephemeral lakes along the Coorong lagoon in southern Australia (von der Borch, 1976;Rosen et al, 1989;Warren, 1990;Wright and Wacey, 2005). Dolomite precipitation is further reported in endorheic hypersaline lakes, e.g., Qinghai Lake in Tibet (Deng et al, 2010), Lake Acıgöl (Turkey;Balci et al, 2016) and alkaline playa lakes such as Deep Springs Lake in California (Meister et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Authigenic formation of Ca–Mg carbonates in the shallow alkaline Lake Neusiedl, Austria

Fussmann¹,

Hoyningen-Huene²,

Reimer³

et al. 2020

Biogeosciences

Self Cite

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Abstract. Despite advances regarding the microbial and organic-molecular impact on nucleation, the formation of dolomite in sedimentary environments is still incompletely understood. Since 1960, apparent dolomite formation has been reported from mud sediments of the shallow, oligohaline and alkaline Lake Neusiedl, Austria. To trace potential dolomite formation or diagenetic alteration processes in its deposits, lake water samples and sediment cores were analyzed with respect to sediment composition, hydrochemistry and bacterial community composition. Sediments comprise 20 cm of homogenous mud with 60 wt % carbonate, which overlies dark-laminated consolidated mud containing 50 wt % carbonate and plant debris. Hydrochemical measurements reveal a shift from oxic lake water with pH 9.0 to anoxic sediment pore water with pH 7.5. A decrease in SO42- with a concomitant increase in ΣH2S and NH4+ from 0 to 15 cm core depth indicates anaerobic heterotrophic decomposition, including sulfate reduction. The bacterial community composition reflects the zonation indicated by the pore water chemistry, with a distinct increase in fermentative taxa below 15 cm core depth. The water column is highly supersaturated with respect to (disordered) dolomite and calcite, whereas saturation indices of both minerals rapidly approach zero in the sediment. Notably, the relative proportions of different authigenic carbonate phases and their stoichiometric compositions remain constant with increasing core depth. Hence, evidence for Ca–Mg carbonate formation or ripening to dolomite is lacking within the sediment of Lake Neusiedl. As a consequence, precipitation of high-magnesium calcite (HMC) and protodolomite does not occur in association with anoxic sediment and sulfate-reducing conditions. Instead, analytical data for Lake Neusiedl suggest that authigenic HMC and protodolomite precipitate from the supersaturated, well-mixed aerobic water column. This observation supports an alternative concept to dolomite formation in anoxic sediments, comprising Ca–Mg carbonate precipitation in the water column under aerobic and alkaline conditions.

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Bacterial succession along a sediment porewater gradient at Lake Neusiedl in Austria

Cited by 23 publications

References 51 publications

A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments

A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments

Local and global chemical shaping of bacterial communities by redox potential

Authigenic formation of Ca–Mg carbonates in the shallow alkaline Lake Neusiedl, Austria

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