Physical map of the genome of Planctomyces limnophilus, a representative of the phylogenetically distinct planctomycete lineage

Enhanced sequestration of molybdenum(VI) using composite constructed wetlands and responses of microbial communities

The molybdenum (Mo) non-point source pollution in the mining area has an irreversible impact on the surrounding water and soil ecosystems. Herein, three integrated vertical subsurface flow constructed wetlands (CWs) were constructed to assess the effects of combination substrates and plant on the removal of Mo(VI). Results showed that CW1 with combination substrates and cattail exhibited a favorable removal performance for Mo(VI) at 80.90%. Moreover, most Mo(VI) retained in the CWs was retained in the substrate (58.13-88.04%), and the largest fraction of Mo(VI) retained was the water-soluble fraction on the surface of the combination substrates. Mo(VI) removal was also influenced by the microbial community composition in substrate, especially their co-occurrence networks. The species that showed significant positive correlation with Mo(VI) removal were Planctomycetes, Latescibacteria, Armatimonadetes, and Gemmatimonadetes. Moreover, CWs added plants showed that more co-occurrences interaction between taxa occurs, which means that the wetlands efficiently select recruitment of potential microbial consortia and change the co-occurrences to remove pollution in the substrate. These results could be useful in providing an ecology-based solution for the treatment of Mo(VI) in wastewater, especially in adjusting the microbial communities for Mo(VI) removal at the genetic level.

Development of Genetic Tools for the Manipulation of the Planctomycetes

Bacteria belonging to the Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) superphylum are of interest for biotechnology, evolutionary cell biology, ecology, and human health. Some PVC species lack a number of typical bacterial features while others possess characteristics that are usually more associated to eukaryotes or archaea. For example, the Planctomycetes phylum is atypical for the absence of the FtsZ protein and for the presence of a developed endomembrane system. Studies of the cellular and molecular biology of these infrequent characteristics are currently limited due to the lack of genetic tools for most of the species. So far, genetic manipulation in Planctomycetes has been described in Planctopirus limnophila only. Here, we show a simple approach that allows mutagenesis by homologous recombination in three different planctomycetes species (i.e., Gemmata obscuriglobus, Gimesia maris, and Blastopirellula marina), in addition to P. limnophila, thus extending the repertoire of genetically modifiable organisms in this superphylum. Although the Planctomycetes show high resistance to most antibiotics, we have used kanamycin resistance genes in G. obscuriglobus, P. limnophila, and G. maris, and tetracycline resistance genes in B. marina, as markers for mutant selection. In all cases, plasmids were introduced in the strains by mating or electroporation, and the genetic modification was verified by Southern Blotting analysis. In addition, we show that the green fluorescent protein (gfp) is expressed in all four backgrounds from an Escherichia coli promoter. The genetic manipulation achievement in four phylogenetically diverse planctomycetes will enable molecular studies in these strains, and opens the door to developing genetic approaches not only in other planctomycetes but also other species of the superphylum, such as the Lentisphaerae.

Characterization of Planctomyces limnophilus and development of genetic tools for its manipulation establish it as a model species for the phylum Planctomycetes

Planctomycetes represent a remarkable clade in the domain Bacteria because they play crucial roles in global carbon and nitrogen cycles and display cellular structures that closely parallel those of eukaryotic cells. Studies on Planctomycetes have been hampered by the lack of genetic tools, which we developed for Planctomyces limnophilus.

Complete genome sequence of Planctomyces limnophilus type strain (Mü 290)

Planctomyces limnophilus Hirsch and Müller 1986 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall which is stabilized by a proteinaceous layer rather than a peptidoglycan layer. Besides Pirellula staleyi, this is the second completed genome sequence of the family Planctomycetaceae. P. limnophilus is of interest because it differs from Pirellula by the presence of a stalk and its structure of fibril bundles, its cell shape and size, the formation of multicellular rosettes, low salt tolerance and red pigmented colonies. The 5,460,085 bp long genome with its 4,304 protein-coding and 66 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Evaluation of the phylogenetic position of the planctomycete 'Rhodopirellula baltica' SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees

In recent years, the planctomycetes have been recognized as a phylum of environmentally important bacteria with habitats ranging from soil and freshwater to marine ecosystems. The planctomycetes form an independent phylum within the bacterial domain, whose exact phylogenetic position remains controversial. With the completion of sequencing of the genome of 'Rhodopirellula baltica' SH 1, it is now possible to re-evaluate the phylogeny of the planctomycetes based on multiple genes and genome trees in addition to single genes like the 16S rRNA or the elongation factor Tu. Here, evidence is presented based on the concatenated amino acid sequences of ribosomal proteins and DNA-directed RNA polymerase subunits from 'Rhodopirellula baltica' SH 1 and more than 90 other publicly available genomes that support a relationship of the Planctomycetes and the Chlamydiae. Affiliation of 'Rhodopirellula baltica' SH 1 and the Chlamydiae was reasonably stable regarding site selection since, during stepwise filtering of less-conserved sites from the alignments, it was only broken when rigorous filtering was applied. In a few cases, 'Rhodopirellula baltica' SH 1 shifted to a deep branching position adjacent to the Thermotoga/Aquifex clade. These findings are in agreement with recent publications, but the deep branching position was dependent on site selection and treeing algorithm and thus not stable. A genome tree calculated from normalized BLASTP scores did not confirm a close relationship of 'Rhodopirellula baltica' SH 1 and the Chlamydiae, but also indicated that the Planctomycetes do not emerge at the very root of the Bacteria. Therefore, these analyses rather contradict a deep branching position of the Planctomycetes within the bacterial domain and reaffirm their earlier proposed relatedness to the Chlamydiae.

Gene discovery within the planctomycete division of the domain Bacteria using sequence tags from genomic DNA libraries

BACKGROUND

The planctomycetes comprise a distinct group of the domain Bacteria, forming a separate division by phylogenetic analysis. The organization of their cells into membrane-defined compartments including membrane-bounded nucleoids, their budding reproduction and complete absence of peptidoglycan distinguish them from most other Bacteria. A random sequencing approach was applied to the genomes of two planctomycete species, Gemmata obscuriglobus and Pirellula marina, to discover genes relevant to their cell biology and physiology.

RESULTS

Genes with a wide variety of functions were identified in G. obscuriglobus and Pi. marina, including those of metabolism and biosynthesis, transport, regulation, translation and DNA replication, consistent with established phenotypic characters for these species. The genes sequenced were predominantly homologous to those in members of other divisions of the Bacteria, but there were also matches with nuclear genomic genes of the domain Eukarya, genes that may have appeared in the planctomycetes via horizontal gene transfer events. Significant among these matches are those with two genes atypical for Bacteria and with significant cell-biology implications - integrin alpha-V and inter-alpha-trypsin inhibitor protein - with homologs in G. obscuriglobus and Pi. marina respectively.

CONCLUSIONS

The random-sequence-tag approach applied here to G. obscuriglobus and Pi. marina is the first report of gene recovery and analysis from members of the planctomycetes using genome-based methods. Gene homologs identified were predominantly similar to genes of Bacteria, but some significant best matches to genes from Eukarya suggest that lateral gene transfer events between domains may have involved this division at some time during its evolution.

The diverse and dynamic structure of bacterial genomes

Bacterial genome sizes, which range from 500 to 10,000 kbp, are within the current scope of operation of large-scale nucleotide sequence determination facilities. To date, 8 complete bacterial genomes have been sequenced, and at least 40 more will be completed in the near future. Such projects give wonderfully detailed information concerning the structure of the organism's genes and the overall organization of the sequenced genomes. It will be very important to put this incredible wealth of detail into a larger biological picture: How does this information apply to the genomes of related genera, related species, or even other individuals from the same species? Recent advances in pulsed-field gel electrophoretic technology have facilitated the construction of complete and accurate physical maps of bacterial chromosomes, and the many maps constructed in the past decade have revealed unexpected and substantial differences in genome size and organization even among closely related bacteria. This review focuses on this recently appreciated plasticity in structure of bacterial genomes, and diversity in genome size, replicon geometry, and chromosome number are discussed at inter- and intraspecies levels.

Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes

The group of planctomycetes represents a separate line of descent within the domain Bacteria. Two phylum-specific 16S rRNA-targeted oligonucleotide probes for planctomycetes have been designed, optimized for in situ hybridization and used in different habitats to detect members of the group in situ. The probes, named PLA46 and PLA886, are targeting all or nearly all members of the planctomycete line of descent. Planctomycetes could be detected in almost all samples examined, e.g. a brackish water lagoon, activated sludge, and other wastewater habitats. In situ probing revealed quite uniform morphology and spatial arrangement of the detected cells but profound differences in abundance ranging from less than 0.1% to several percentage of the total cells. Single coccoid cells with diameters between 1 and 2.5 microm were dominating in most samples with the exception of the lagoon, in which rosettes of pear-shaped cells were abundant. The planctomycetes showed generally no hybridization signals with the bacterial probe EUB338, which is in accordance with base changes in their 165 rRNA sequences. A discrete ultrastructure of planctomycete cells was suggested by double staining with rRNA-targeted probes and the DNA-binding dye 4',6-diamidino-2-phenylindole (DAPI). The probe-conferred fluorescence was distributed in a ring-shaped manner around a central DAPI spot. The two probes developed extend the existing set of group-specific rRNA-targeted probes and help to elucidate the basic composition of bacterial communities in a first step of differential analysis. In situ hybridization of environmental samples indicated widespread presence of planctomycetes in different ecosystems.

Cloning and characterization of Planctomyces limnophilus rpoN: complementation of a Salmonella typhimurium rpoN mutant strain

The rpoN gene, which encodes the alternative sigma factor sigma 54, was cloned from the budding, peptidoglycan-less bacterium Planctomyces limnophilus. P. limnophilus rpoN complemented the Ntr- phenotype of a Salmonella typhimurium rpoN mutant strain. The P. limnophilus rpoN gene encoded a predicted polypeptide that was 495 residues in length and shared a significant homology with other members of the sigma 54 family. The protein sequence displayed all of the characteristic motifs found in members of this family, including the C-terminal helix-turn-helix motif and the well-conserved RpoN box. A potential sigma 54-dependent activator was also identified in P. limnophilus. These findings extend the range of phylogenetic groups within the Domain Bacteria that are known to contain sigma 54.

The presence of a dnaK (HSP70) multigene family in members of the orders Planctomycetales and Verrucomicrobiales

Sequences of the dnaK gene, coding for the 70-kDa heat shock protein (HSP70), were determined for six members of the order Planctomycetales, including representatives of three genera, and for the only cultivated member of the order Verrucomicrobiales, Verrucomicrobium spinosum. A fragment of the dnaK gene was amplified from these strains by PCR with oligonucleotide primers targeting regions of the dnaK gene that are conserved at the amino acid level, and the resulting PCR products were cloned into a plasmid vector. Sequence analysis of the cloned dnaK fragments revealed the presence of two different types of dnaK sequence in one of the planctomycete strains, Planctomyces maris, and in V. spinosum. Only one type of dnaK sequence was found for each of the remaining strains. Phylogenetic analysis of the partial sequence data suggested that the majority of planctomycete strains, including one of the Planctomyces maris sequences, form a coherent phylogenetic group branching adjacent to other main lines of descent within the domain Bacteria, as has been shown previously by 16S rRNA sequence analysis. One of the two V. spinosum dnaK sequences also appears to constitute a separate lineage within the gram-negative bacteria. Each of the remaining sequences from P. maris and V. spinosum, together with the single sequence obtained from Planctomyces limnophilus, appeared to be unrelated to the other planctomycete sequences and to occupy a position distant from that of other gram-negative bacteria. The phylogenetic diversity of dnaK sequences exhibited by P. maris and V. spinosum was comparable to that found in Synechococcus sp. strain PCC7942 and Escherichia coli, the only other prokaryotes for which a dnaK multigene family has been demonstrated.