Rhodoferax saidenbachensis sp. nov., a psychrotolerant, very slowly growing bacterium within the family Comamonadaceae, proposal of appropriate taxonomic position of Albidiferax ferrireducens strain T118T in the genus Rhodoferax and emended description of the genus Rhodoferax

Kaden, René; Spröer, Cathrin; Beyer, Dániel; Krolla-Sidenstein, Peter

doi:10.1099/ijs.0.054031-0

Cited by 41 publications

(26 citation statements)

References 37 publications

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“…Six OTUs were annotated as Proteobacteria (2 α, 3 β and 1 ε): Rhodoferax MS_1, Brevundimonas MS_2, Polynucleobacter duraquae_1, Comamonadaceae MG_12, Bordetella_1 and Helicobacter_typhlonius_1. Rhidoferax MS_1 could be annotated as either Rhodoferax ferrireducens or Rhodoferax saidenbachensis [strains T118 and ED16 respectively (Kaden et al ., )], which share common 16S rRNA gene sequence at this amplified region. Both are psychrotolerant (can grow at 4 °C, although not pyschorophilic) bacteria commonly isolated from water; however, it is interesting that R. ferrireducens was transported to the space station as part of the first bacterial fuel cell experiments on the ISS [exhibition 8 (De Vet and Rutgers, )].…”

Section: Resultsmentioning

confidence: 99%

ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples

González

Pitre

Brereton

2019

Environmental Microbiology

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SummaryAnalysis of 16S ribosomal RNA (rRNA) gene amplification data for microbial barcoding can be inaccurate across complex environmental samples. A method, ANCHOR, is presented and designed for improved species‐level microbial identification using paired‐end sequences directly, multiple high‐complexity samples and multiple reference databases. A standard operating procedure (SOP) is reported alongside benchmarking against artificial, single sample and replicated mock data sets. The method is then directly tested using a real‐world data set from surface swabs of the International Space Station (ISS). Simple mock community analysis identified 100% of the expected species and 99% of expected gene copy variants (100% identical). A replicated mock community revealed similar or better numbers of expected species than MetaAmp, DADA2, Mothur and QIIME1. Analysis of the ISS microbiome identified 714 putative unique species/strains and differential abundance analysis distinguished significant differences between the Destiny module (U.S. laboratory) and Harmony module (sleeping quarters). Harmony was remarkably dominated by human gastrointestinal tract bacteria, similar to enclosed environments on earth; however, Destiny module bacteria also derived from nonhuman microbiome carriers present on the ISS, the laboratory's research animals. ANCHOR can help substantially improve sequence resolution of 16S rRNA gene amplification data within biologically replicated environmental experiments and integrated multidatabase annotation enhances interpretation of complex, nonreference microbiomes.

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Section: Resultsmentioning

confidence: 99%

ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples

González

Pitre

Brereton

2019

Environmental Microbiology

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“…The cultivated lineage most closely related to the abundant iron mat OTU is the iron-reducing bacterium Rhodoferax ferrireducens (23). However, the genus Rhodoferax is metabolically diverse, consisting of species that carry out anoxygenic photosynthesis and chemotrophy (24); furthermore, members of the family Comamonadaceae, which includes Leptothrix species, exhibit a wide range of physiologies (25). Thus, the metabolic function(s) of these prevalent Comamonadaceae OTUs is unclear, and given the diversity of different oligotypes, it is possible there are different strains with different metabolisms.…”

Section: Discussionmentioning

confidence: 99%

Microbial Iron Oxidation in the Arctic Tundra and Its Implications for Biogeochemical Cycling

Emerson

Scott

Beneš

et al. 2015

Appl Environ Microbiol

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The role that neutrophilic iron-oxidizing bacteria play in the Arctic tundra is unknown. This study surveyed chemosynthetic iron-oxidizing communities at the North Slope of Alaska near Toolik Field Station (TFS) at Toolik Lake (lat 68.63, long ؊149.60). Microbial iron mats were common in submerged habitats with stationary or slowly flowing water, and their greatest areal extent is in coating plant stems and sediments in wet sedge meadows. Some Fe-oxidizing bacteria (FeOB) produce easily recognized sheath or stalk morphotypes that were present and dominant in all the mats we observed. The cool water temperatures (9 to 11°C) and reduced pH (5.0 to 6.6) at all sites kinetically favor microbial iron oxidation. A microbial survey of five sites based on 16S rRNA genes found a predominance of Proteobacteria, with Betaproteobacteria and members of the family Comamonadaceae being the most prevalent operational taxonomic units (OTUs). In relative abundance, clades of lithotrophic FeOB composed 5 to 10% of the communities. OTUs related to cyanobacteria and chloroplasts accounted for 3 to 25% of the communities. Oxygen profiles showed evidence for oxygenic photosynthesis at the surface of some mats, indicating the coexistence of photosynthetic and FeOB populations. The relative abundance of OTUs belonging to putative Fe-reducing bacteria (FeRB) averaged around 11% in the sampled iron mats. Mats incubated anaerobically with 10 mM acetate rapidly initiated Fe reduction, indicating that active iron cycling is likely. The prevalence of iron mats on the tundra might impact the carbon cycle through lithoautotrophic chemosynthesis, anaerobic respiration of organic carbon coupled to iron reduction, and the suppression of methanogenesis, and it potentially influences phosphorus dynamics through the adsorption of phosphorus to iron oxides. The Arctic tundra biome is fascinating in its own right and has the potential to be heavily affected by changes in climate associated with increased atmospheric CO 2 concentrations and global warming. One of the most dramatic impacts is likely to be a change in the dynamics of permanently frozen soils (permafrost) as overall temperatures rise and the shoulder seasons of thaw and freeze-up expand (1-3). Understanding the biogeochemical implications of climate change in the Arctic is important, in part because relative to its total landmass area, permafrost stores an outsized fraction of organic carbon (4). The fate of that carbon, especially the portion that is mineralized to CO 2 and/or methane, has the potential to impact further climate change through the release of greenhouse gases. Understanding the range of biogeochemical processes in the Arctic and how they impact the carbon cycle, either directly or indirectly, is thus of vital importance.In general, the microbial iron cycle in the Arctic tundra is poorly understood. Only in the past few years have studies started to investigate the reductive aspects of the iron cycle, which have shown that Fe-reducing bacteria can account for a large fracti...

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“…The betaproteobacterium OTU that dominated the surface water of the lake ( Figure 8B) had closest sequence similarity to R. saidenbachensis, a non-photosynthetic, strictly aerobic, psychrotolerant species which has been described from the sediments of a temperate lake (Kaden et al, 2014). Based on related environmental sequences, these researchers speculated that it has an affinity for low-nutrient environments, which would be the case for Milne Fiord epishelf lake.…”

Section: Microbial Community Compositionmentioning

confidence: 99%

Microbial Community Structure and Interannual Change in the Last Epishelf Lake Ecosystem in the North Polar Region

et al. 2017

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Climate warming is proceeding rapidly in the polar regions, posing a threat to ice-dependent ecosystems. Among the most vulnerable are microbial-dominated epishelf lakes, in which surface ice-damming of an embayment causes a freshwater layer to overlie the sea, creating an interface between distinct habitats. We characterized the physicochemical and biotic environment of Milne Fiord epishelf lake (82 • N, Canada) in three successive summers (2010)(2011)(2012), and on one date of profiling (5 July 2011) we collected samples for high through-put amplicon sequencing of variable regions of small subunit rRNA to characterize the microbial community (Eukarya, Bacteria and Archaea). Potentially active water column communities were investigated using reverse-transcribed rRNA, and phytoplankton were further characterized by accessory pigment analysis. Cluster analysis of pigment data showed a demarcation between freshwater and marine communities, which was also evident in the sequence data. The halocline community of Eukarya was more similar to the deeper marine sample than to the freshwater surface community, while the Archaea and Bacteria communities at this interface clustered more with surface communities. In 2012, conductivity-depth profiles indicated shallowing of the freshwater layer and mixing across the halocline, accompanied by lower picocyanobacteria and higher picoeukaryote concentrations. Picocyanobacteria cells were more evenly distributed throughout the water column in 2012, implying partial deep mixing. Several mixotrophic taxa of Eukarya were more abundant in the freshwater layer, where low nutrient concentrations may favor this lifestyle. Unusual features of Milne Fiord microbial communities included benthic taxa not previously reported in marine water columns (notably, the archaeon Halobacteriales), and dominance by taxa that are typically present in sparse concentrations elsewhere: for example, the Chlorophyte group Radicarteria and the betaproteobacterium Rhodoferax.Thaler et al. Microbial Communities in an Ice-Dammed Arctic LakeMilne Fiord epishelf lake is the last known lake of this kind remaining in the Arctic, and the fate of this distinct microbial ecosystem may ultimately depend on the stability of the Milne Fiord ice shelf, which has experienced a negative mass balance over the past half century.

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Rhodoferax saidenbachensis sp. nov., a psychrotolerant, very slowly growing bacterium within the family Comamonadaceae, proposal of appropriate taxonomic position of Albidiferax ferrireducens strain T118T in the genus Rhodoferax and emended description of the genus Rhodoferax

Cited by 41 publications

References 37 publications

ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples

ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples

Microbial Iron Oxidation in the Arctic Tundra and Its Implications for Biogeochemical Cycling

Microbial Community Structure and Interannual Change in the Last Epishelf Lake Ecosystem in the North Polar Region

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