A New Species of Azotobacter

Starkey, Robert L.; De, P. K.

doi:10.1097/00010694-193904000-00007

Cited by 28 publications

(10 citation statements)

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“…Organisms and genome sequencing Genomes were obtained from M. silvestris BL2 (Starkey and De, 1939) grows on diverse multicarbon compounds, but does not oxidize methane or methanol (Kennedy, 2005;Dedysh, Smirnova et al, 2005). M. silvestris is the facultative methanotroph with the widest known range of energy substrates .…”

Section: Methodsmentioning

confidence: 99%

The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis

Tamaš

Smirnova

et al. 2013

The ISME Journal

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The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) viaLGT. This was supported by a compositional analysis suggesting that all MMOs in Alphaproteobacteria methanotrophs are foreign in origin. Some members of the Beijerinckiaceae subsequently lost methanotrophic functions and regained the ability to grow on multicarbon energy substrates. We conclude that B. indica is a recidivist multitroph, the only known example of a bacterium having completely abandoned an evolved lifestyle of specialized methanotrophy.

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Section: Methodsmentioning

confidence: 99%

The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis

Tamaš

Smirnova

et al. 2013

The ISME Journal

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“…In contrast, Methylocapsa acidiphila is capable of exponential growth in liquid nitrogen-free media under both aerobic and microaerobic conditions (Dedysh et al, 2002). This growth capability of Methylocapsa acidiphila is very similar to that of Beijerinckia, which was one of the first bacteria described as being capable of fixing dinitrogen effectively (Alston, 1936;Starkey & De, 1939;Becking, 1999).…”

Section: Introductionmentioning

confidence: 98%

NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria

2004

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The ability to utilize dinitrogen as a nitrogen source is an important phenotypic trait in most currently known methanotrophic bacteria (MB). This trait is especially important for acidophilic MB, which inhabit acidic oligotrophic environments, highly depleted in available nitrogen compounds. Phylogenetically, acidophilic MB are most closely related to heterotrophic dinitrogen-fixing bacteria of the genus Beijerinckia. To further explore the phylogenetic linkage between these metabolically different organisms, the sequences of nifH and nifD gene fragments from acidophilic MB of the genera Methylocella and Methylocapsa, and from representatives of Beijerinckia, were determined. For reference, nifH and nifD sequences were also obtained from some type II MB of the alphaproteobacterial Methylosinus/Methylocystis group and from gammaproteobacterial type I MB. The trees constructed for the inferred amino acid sequences of nifH and nifD were highly congruent. The phylogenetic relationships among MB in the NifH and NifD trees also agreed well with the corresponding 16S rRNA-based phylogeny, except for two distinctive features. First, different methods used for phylogenetic analysis grouped the NifH and NifD sequences of strains of the gammaproteobacterial MB Methylococcus capsulatus within a clade mainly characterized by Alphaproteobacteria, including acidophilic MB and type II MB of the Methylosinus/Methylocystis group. From this and other genomic data from Methylococcus capsulatus Bath, it is proposed that an ancient event of lateral gene transfer was responsible for this aberrant branching. Second, the identity values of NifH and NifD sequences between Methylocapsa acidiphila B2 and representatives of Beijerinckia were clearly higher (98?5 and 96?6 %, respectively) than would be expected from their 16S rRNA-based relationships. Possibly, these two bacteria originated from a common acidophilic dinitrogen-fixing ancestor, and were subject to similar evolutionary pressure with regard to nitrogen acquisition. This interpretation is corroborated by the observation that, in contrast to most other diazotrophs, M. acidiphila B2 and Beijerinckia spp. are capable of active growth on nitrogen-free media under fully aerobic conditions.

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“…indica (ATCC 9039) is known for its copious production of EPS (18). Most of the EPS produced (85 to 90%) is an acidic heteropolysaccharide comprised of repeating subunits of [L-guluronic acid, ␤(1¡3) D-glucose, and ␤(1¡4) D-glycero-D-mannoheptose ␤(1¡4)] (19,20).…”

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confidence: 99%

Stable-Isotope Probing Identifies Uncultured Planctomycetes as Primary Degraders of a Complex Heteropolysaccharide in Soil

Wang

Sharp

Jones

et al. 2015

Appl Environ Microbiol

106

162

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The exopolysaccharides (EPSs) produced by some bacteria are potential growth substrates for other bacteria in soil. We used stable-isotope probing (SIP) to identify aerobic soil bacteria that assimilated the cellulose produced by Gluconacetobacter xylinus or the EPS produced by Beijerinckia indica. The latter is a heteropolysaccharide comprised primarily of L-guluronic acid, D-glucose, and D-glycero-D-mannoheptose.13 C-labeled EPS and 13 C-labeled cellulose were purified from bacterial cultures grown on [ 13 C]glucose. Two soils were incubated with these substrates, and bacteria actively assimilating them were identified via pyrosequencing of 16S rRNA genes recovered from 13 C-labeled DNA. Cellulose C was assimilated primarily by soil bacteria closely related (93 to 100% 16S rRNA gene sequence identities) to known cellulose-degrading bacteria. However, B. indica EPS was assimilated primarily by bacteria with low identities (80 to 95%) to known species, particularly by different members of the phylum Planctomycetes. In one incubation, members of the Planctomycetes made up >60% of all reads in the labeled DNA and were only distantly related (<85% identity) to any described species. Although it is impossible with SIP to completely distinguish primary polysaccharide hydrolyzers from bacteria growing on produced oligo-or monosaccharides, the predominance of Planctomycetes suggested that they were primary degraders of EPS. Other bacteria assimilating B. indica EPS included members of the Verrucomicrobia, candidate division OD1, and the Armatimonadetes. The results indicate that some uncultured bacteria in soils may be adapted to using complex heteropolysaccharides for growth and suggest that the use of these substrates may provide a means for culturing new species. Some major phyla of the domain Bacteria, like the Proteobacteria and Actinobacteria, are well-known from cultivation studies. Others, like Acidobacteria, Verrucomicrobia, and Planctomycetes, have few cultured species, although they make up large proportions of the bacterial 16S rRNA genes detected in environments such as soil (1). One theory proposed to explain the difficulty in culturing bacteria from these phyla is that most are K selected as opposed to r selected. Typical r-selected bacteria grow rapidly on simple monomeric substrates in nutrient-rich environments, conditions presented by most microbiological media (2, 3). On the other hand, K-selected bacteria have a more efficient cell metabolism and strong competitive ability and grow slowly on recalcitrant, complex substances (3-5). Several studies have demonstrated that members of difficult-to-culture phyla like Acidobacteria, Verrucomicrobia, and Planctomycetes can be cultivated using polysaccharides, such as xylan, xanthan, and pectin, as energy sources (e.g., see references 6 to 8). The heteropolysaccharide gellan, which is often used as a gelling agent as an alternative to agar, can also act as an energy source for some soil bacteria (9), in part explaining the observation that it improves cultu...

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A New Species of Azotobacter

Cited by 28 publications

References 0 publications

The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis

The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis

NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria

Stable-Isotope Probing Identifies Uncultured Planctomycetes as Primary Degraders of a Complex Heteropolysaccharide in Soil

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