Phycisphaera mikurensis gen. nov., sp. nov., isolated from a marine alga, and proposal of Phycisphaeraceae fam. nov., Phycisphaerales ord. nov. and Phycisphaerae classis nov. in the phylum Planctomycetes

Fukunaga, Yukiyo; Kurahashi, Midori; Sakiyama, Yayoi; Ohuchi, Motoyuki; Yokota, Akira; Harayama, Shigeaki

doi:10.2323/jgam.55.267

Cited by 193 publications

(155 citation statements)

References 42 publications

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“…The genus Gemmatimonas (phyluma Gemmatimanadetes) is known for having members with active roles in biogeochemical transformations in hypersaline soils (Zhang et al 2003). The genera Phycisphaera and Planctomyces (phylum Planctomycetes) are symbionts of marine algae or sponges (Fukunaga et al 2009;Jogler et al 2011). Although more than 100 sequences were assigned to the genus Pyramidobacter in the present study, this genus has not previously been reported in saline habitats.…”

Section: Bacteriamentioning

confidence: 54%

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

Gong

2013

World J Microbiol Biotechnol

102

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An integrated view of bacterial and archaeal diversity in saline soil habitats is essential for understanding the biological and ecological processes and exploiting potential of microbial resources from such environments. This study examined the collective bacterial and archaeal diversity in saline soils using a meta-analysis approach. All available 16S rDNA sequences recovered from saline soils were retrieved from publicly available databases and subjected to phylogenetic and statistical analyses. A total of 9,043 bacterial and 1,039 archaeal sequences, each longer than 250 bp, were examined. The bacterial sequences were assigned into 5,784 operational taxonomic units (OTUs, based on C97 % sequence identity), representing 24 known bacterial phyla, with Proteobacteria (44.9 %), Actinobacteria (12.3 %), Firmicutes (10.4 %), Acidobacteria (9.0 %), Bacteroidetes (6.8 %), and Chloroflexi (5.9 %) being predominant. Lysobacter (12.8 %) was the dominant bacterial genus in saline soils, followed by Sphingomonas (4.5 %), Halomonas (2.5 %), and Gemmatimonas (2.5 %). Archaeal sequences were assigned to 602 OTUs, primarily from the phyla Euryarchaeota (88.7 %) and Crenarchaeota (11.3 %).Halorubrum and Thermofilum were the dominant archaeal genera in saline soils. Rarefaction analysis indicated that less than 25 % of bacterial diversity, and approximately 50 % of archaeal diversity, in saline soil habitats has been sampled. This analysis of the global bacterial and archaeal diversity in saline soil habitats can guide future studies to further examine the microbial diversity of saline soils.

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Section: Bacteriamentioning

confidence: 54%

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

Gong

2013

World J Microbiol Biotechnol

102

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“…There are only a few cultured species of Planctomycetes available, and knowledge of the overall diversity of this phylum is therefore limited. The phylum has two validated classes: the Planctomycetacia, which contains 11 genera, and the Phycisphaerae, formerly known as the WPS1 group (44,45), which contains the single genus and species Phycisphaera mikurensis (46). In addition, some "Candidatus Planctomycetes" species are anaerobic ammonium-oxidizing (anammox) bacteria consisting of lithoautotrophs that reduce nitrite and oxidize ammonium to produce dinitrogen gas under anoxic conditions (45).…”

Section: -37) Previous Studies Also Commonly Identifiedmentioning

confidence: 99%

“…Aside from the anammox bacteria, most cultured Planctomycetes, including Phycisphaera mikurensis, the only cultured representative of the Phycisphaerae, are organoheterotrophs. Few polymeric growth substrates have been tested on this organism, although it can grow on cellobiose and several monosaccharides (46). Members of the Phycisphaerae have been found to be associated with polymeric substrates, such as decaying wood (47).…”

Section: -37) Previous Studies Also Commonly Identifiedmentioning

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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“…The phyla Planctomycetes and Verrucomicrobia are closely related; they are united by their morphological similarity, in particular intracellular membrane organization (27,28), and were among the first bacteria to challenge the view that bacteria are simple organisms lacking organizational complexity. The planctomycetes form three distinct clades: autotrophic species that contain the anammoxosome (reviewed by van Niftrik and Jetten [29]); the class Phycisphaerae, which are facultative aerobes and divide by binary fission (30); and the class Planctomycetia, members of which are predominantly aerobic or facultatively aerobic, lack anammoxosomes, and divide by budding. Nine members from the last clade representing seven genera isolated from very different habitats have sequenced genomes; eight contain the BMC gene cluster.…”

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confidence: 99%

Characterization of a Planctomycetal Organelle: a Novel Bacterial Microcompartment for the Aerobic Degradation of Plant Saccharides

Erbilgin

McDonald

Kerfeld

2014

Appl Environ Microbiol

126

142

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Bacterial microcompartments (BMCs) are organelles that encapsulate functionally linked enzymes within a proteinaceous shell. The prototypical example is the carboxysome, which functions in carbon fixation in cyanobacteria and some chemoautotrophs. It is increasingly apparent that diverse heterotrophic bacteria contain BMCs that are involved in catabolic reactions, and many of the BMCs are predicted to have novel functions. However, most of these putative organelles have not been experimentally characterized. In this study, we sought to discover the function of a conserved BMC gene cluster encoded in the majority of the sequenced planctomycete genomes. This BMC is especially notable for its relatively simple genetic composition, its remote phylogenetic position relative to characterized BMCs, and its apparent exclusivity to the enigmatic Verrucomicrobia and Planctomycetes. Members of the phylum Planctomycetes are known for their morphological dissimilarity to the rest of the bacterial domain: internal membranes, reproduction by budding, and lack of peptidoglycan. As a result, they are ripe for many discoveries, but currently the tools for genetic studies are very limited. We expanded the genetic toolbox for the planctomycetes and generated directed gene knockouts of BMC-related genes in Planctomyces limnophilus. A metabolic activity screen revealed that BMC gene products are involved in the degradation of a number of plant and algal cell wall sugars. Among these sugars, we confirmed that BMCs are formed and required for growth on L-fucose and L-rhamnose. Our results shed light on the functional diversity of BMCs as well as their ecological role in the planctomycetes, which are commonly associated with algae.

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Phycisphaera mikurensis gen. nov., sp. nov., isolated from a marine alga, and proposal of Phycisphaeraceae fam. nov., Phycisphaerales ord. nov. and Phycisphaerae classis nov. in the phylum Planctomycetes

Cited by 193 publications

References 42 publications

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

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

Characterization of a Planctomycetal Organelle: a Novel Bacterial Microcompartment for the Aerobic Degradation of Plant Saccharides

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