Skip to main content
PMC home page
Springer logoLink to Springer
. 2020 May 12;113(12):1889–1900. doi: 10.1007/s10482-020-01424-3

Tautonia plasticadhaerens sp. nov., a novel species in the family Isosphaeraceae isolated from an alga in a hydrothermal area of the Eolian Archipelago

Christian Jogler 1,2,✉, Sandra Wiegand 3, Christian Boedeker 4, Anja Heuer 4, Stijn H Peeters 1, Mareike Jogler 2, Mike S M Jetten 1, Manfred Rohde 5, Nicolai Kallscheuer 1
PMCID: PMC7716859  PMID: 32399714

Abstract

A novel planctomycetal strain, designated ElPT, was isolated from an alga in the shallow hydrothermal vent system close to Panarea Island in the Tyrrhenian Sea. Cells of strain ElPT are spherical, form pink colonies and display typical planctomycetal characteristics including division by budding and presence of crateriform structures. Strain ElPT has a mesophilic (optimum at 30 °C) and neutrophilic (optimum at pH 7.5) growth profile, is aerobic and heterotrophic. It reaches a generation time of 29 h (µmax = 0.024 h−1). The strain has a genome size of 9.40 Mb with a G + C content of 71.1% and harbours five plasmids, the highest number observed in the phylum Planctomycetes thus far. Phylogenetically, the strain represents a novel species of the recently described genus Tautonia in the family Isosphaeraceae. A characteristic feature of the strain is its tendency to attach strongly to a range of plastic surfaces. We thus propose the name Tautonia plasticadhaerens sp. nov. for the novel species, represented by the type strain ElPT (DSM 101012T = LMG 29141T).

Keywords: Marine bacteria, Panarea, Biotic surfaces, Planctomycetes, Isosphaeraceae, Hydrothermal vent system

Introduction

The phylum Planctomycetes, along with Chlamydiae, Verrucomicrobia and others, forms the PVC superphylum, which is of environmental, medical and biotechnological importance (Spring et al. 2016; Wagner and Horn 2006). Members of the phylum Planctomycetes occur in a broad range of habitats on Earth, with the largest number of species so far isolated from aquatic environments (Wiegand et al. 2018). Phylogenetically, the phylum is subdivided into the classes Phycisphaerae, Planctomycetia and Candidatus Brocadiae. Recent rearrangements in the class Planctomycetia led to a more strictly defined order Planctomycetales and the introduction of the orders Pirellulales, Gemmatales and Isosphaerales (Dedysh et al. 2019). Species of the class Planctomycetia divide by budding, whereas members of the class Phycipshaerae divide by binary fission. Genome size ranges of 3–12 Mb and a G + C content of 40–71% have been observed in characterised strains of the phylum Planctomycetes (Ravin et al. 2018; Wiegand et al. 2020).

Strains clustering within Planctomycetia, the class with the currently highest number of characterised species in the phylum, have been shown to attach to various marine biotic surfaces, e.g. macroscopic phototrophs (Boersma et al. 2019; Bondoso et al. 2014, 2017; Peeters et al. 2020; Vollmers et al. 2017), on which they can be highly abundant (Bengtsson and Øvreås 2010). Such surfaces are suggested to serve as nutrient source, e.g. in the form of complex polysaccharides (Jeske et al. 2013; Lachnit et al. 2013). However, the survival of planctomycetal species appears counter-intuitive given their rather slow growth compared to natural competitors in this ecological niche (Frank et al. 2014; Wiegand et al. 2018). Strategies applied to compensate for lower growth rates may include the ability to produce bioactive secondary metabolites (Kallscheuer et al. 2019c; Panter et al. 2019), resistance against several antibiotics (Cayrou et al. 2010; Godinho et al. 2019) and/or a metabolism well-adapted to digestion of algae-derived compounds, including the above-mentioned polysaccharides. In this context, pili originating from conspicuous crateriform structures and an extremely enlarged periplasmic space observed in Planctomycetes may be involved in the uptake and intracellular cleavage of polymeric carbon sources, as shown for the model substrate dextran (Boedeker et al. 2017).

The cell envelope architecture of species of the phylum Planctomycetes was investigated based on super-resolution microscopic techniques and developed genetic tools (Jogler et al. 2011; Jogler and Jogler 2013; Rivas-Marin et al. 2016), which confirmed presence of peptidoglycan (Jeske et al. 2015; van Teeseling et al. 2015) and a cell envelope similar to that of Gram-negative bacteria (Boedeker et al. 2017; Devos 2014). However, in contrast to canonical bacteria, Planctomycetes lack otherwise essential divisome proteins, including FtsZ (Jogler et al. 2012; Pilhofer et al. 2008). In their genomes, 40–55% of the automatically annotated genes are of unknown function (Wiegand et al. 2020), which is a strong motivation to study the planctomycetal cell biology in greater detail.

To extend the collection of axenic cultures of Planctomycetes and as a basis for further study of their cell biology and metabolism, here we describe a novel strain, ElPT, isolated from an alga sampled in the Tyrrhenian Sea close to the island Panarea.

Materials and methods

Isolation of the novel strain and cultivation

For the isolation and cultivation of strain ElPT, M1H NAG ASW medium was used. Liquid and solid M1H NAG ASW medium was prepared as previously described (Boersma et al. 2019). Strain ElPT was isolated from an alga gathered from hydrothermal area A26 (location: 38.6392 N 15.1051 E). With an average depth of 26 m, A26 is the deepest spot of a plateau located between the small islands Le Guglie and Lisca Bianca around 2.5 km east of the island Panarea, Italy. The geology of area A26 in the shallow-marine hydrothermal system close to Panarea is described elsewhere (Kürzinger 2019). Algal pieces were sampled on the 10th of September 2013 at a depth of 25 m and a water temperature of 19.4 °C. The sampled material was initially washed with sterile seawater containing 20 mg/L cycloheximide to prevent fungal growth. Afterwards, washed algal pieces were swabbed over a plate with M1H NAG ASW medium containing 8 g/L gellan gum, 1000 mg/L streptomycin, 200 mg/L ampicillin and 20 mg/L cycloheximide, which was subsequently incubated at 20 °C for four weeks. The 16S rRNA gene of the strains obtained was amplified by PCR with the primers 8f (5′-AGA GTT TGA TCM TGG CTC AG-3′) and 1492r (5′-GGY TAC CTT GTT ACG ACT T-3′) and then sequenced following a previously published protocol (Rast et al. 2017). This step was performed in order to check whether isolated strains represent members of the phylum Planctomycetes.

Determination of pH and temperature optimum

The pH optimum and range were determined in M1H NAG ASW medium at 28 °C. The following buffers (each 100 mM) were used: 2-(N-morpholino)ethanesulfonic acid (MES) for pH 5.0 and 6.0, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) for pH 7.0, 7.5 and 8.0, 3-(4-(2-hydroxyethyl)piperazin-1-yl)propane-1-sulfonic acid) (HEPPS) for pH 8.5 and N-cyclohexyl-2-aminoethanesulfonic acid (CHES) for pH 9.0 and 10.0. The temperature optimum and range were determined in standard M1H NAG ASW medium at pH 7.5. Growth was assessed by measuring the optical density at 600 nm (OD600). The average of OD600 values from three biological replicates was used for calculation of the growth rates. To this end, the natural logarithm of average OD600 values (ln(OD600)) was plotted against the cultivation time. The slope of the linear range of the curve (at least five data points) was used as maximal growth rate µ (in h−1). The generation time td (in h) was calculated using the equation td = ln(2)/µ.

Microscopy protocols

Phase contrast and field emission scanning electron microscopy were performed as previously described (Boersma et al. 2019).

Genome information and analysis of genome-encoded features

Genome and plasmid sequences of strain ElPT are available from GenBank under accession numbers CP036426–CP036431. The 16S rRNA gene sequence of strain ElPT can be found under accession number MK559970. DNA isolation and genome sequencing was carried out as part of a previous study (Wiegand et al. 2020). Numbers of carbohydrate-active enzymes were obtained from the CAZY database (Lombard et al. 2014). Gene clusters potentially involved in the production of secondary metabolites were determined using antiSMASH 4.0 (Blin et al. 2017).

Phylogenetic analysis

16S rRNA gene sequence-based phylogeny was computed for strain ElPT, the type strains of all described planctomycetal species (assessed in January 2020) and all isolates published in the recent year (Boersma et al. 2019; Kallscheuer et al. 2019a, b, d; Kohn et al. 2019; Kovaleva et al. 2019; Peeters et al. 2020; Rensink et al. 2020) as previously described (Kallscheuer et al. 2019d). Three 16S rRNA genes of bacterial strains from the PVC superphylum, but outside of the phylum Planctomycetes (accession numbers AJ229235, NR_146840 and NR_027571), were used as the outgroup. The multi-locus sequence analysis (MLSA) was performed according to a previously published protocol (Kallscheuer et al. 2019d). The genomes of Gemmata obscuriglobus (accession number CP042911), Rhodopirellula baltica (accession number BX119912.1) and Gimesia maris (accession number CP043931) served as outgroup. The average nucleotide identity (ANI) was calculated using OrthoANI (Lee et al. 2016). The average amino acid identity (AAI) was obtained using the aai.rb script of the enveomics collection (Rodriguez-R and Konstantinidis 2016), while the percentage of conserved proteins (POCP) was calculated as described by Qin et al. (2014). The rpoB nucleotide sequences were taken from publicly available planctomycetal genome annotations and the sequence identities for the described 1200 bp sequence fragment were determined as previously described (Bondoso et al. 2013). Alignment and matrix calculation were performed with Clustal Omega (Sievers et al. 2011).

Results and discussion

Phylogenetic analysis

In both, the 16S rRNA gene sequence- and the MLSA-based phylogenetic tree (Fig. 1), strain ElPT clusters monophyletically with Tautonia sociabilis GM2012T (Kovaleva et al. 2019). The two strains share a 16S rRNA gene sequence similarity of 96.5% (Fig. 2), which is above the recommended genus threshold of 94.5%, but below the species threshold of 98.7% (Stackebrandt and Ebers 2006; Yarza et al. 2014). Comparison at the 16S rRNA gene level thus suggests that strain ElPT represents a novel species in the genus Tautonia, family Isosphaeraceae. This finding is in line with an ANI of 79.8% obtained during comparison of strain ElPT and T. sociabilis, since this value is below the threshold of 95% for strains belonging to the same species (Kim et al. 2014). For a more extensive evaluation, additional phylogenetic markers were taken into account. Indeed, affiliation of strain ElPT to the genus Tautonia and simultaneous delineation from T. sociabilis is supported by AAI, rpoB similarity and POCP values of 76.3%, 90.5% and 65.7%, respectively (Fig. 2). These values fall above the recommended genus thresholds of 60–80% (AAI), 75.5–78% (rpoB) and 50% (POCP) for delineation of prokaryotic genera, but below the thresholds of 95% (AAI) and 96.3% (rpoB) for differentiation of species (Kallscheuer et al. 2019d; Konstantinidis and Tiedje 2005; Qin et al. 2014). T. sociabilis was clearly established as the current closest relative of strain ElPT since lower similarity values were obtained for comparison with species of other known genera in the family Isosphaeraceae, namely Isosphaera, Singulisphaera, Aquisphaera, Paludisphaera and Tundrisphaera. For comparison of strain ElPT with species of the mentioned genera, AAI and 16S rRNA gene similarity values are below the genus threshold, while in most cases the POCP was found to be at or slightly above the genus threshold of 50% (Fig. 2). Similarity of rpoB is used as phylogenetic marker in the order Planctomycetales (Bondoso et al. 2013) and a genus threshold of 75.5–78% was recently proposed based on new strains in the family Pirellulaceae (former members of Planctomycetaceae) (Kallscheuer et al. 2019d). Based on the obtained values (Fig. 2), the rpoB genus threshold is probably not applicable to the family Isosphaeraceae.

Fig. 1.

Fig. 1

Open in a new tab

Maximum likelihood phylogenetic analysis. Phylogenetic trees showing the position of strain ElPT. 16S rRNA gene sequence-(a) and MLSA-based (b) phylogeny was computed as described in the “Materials and methods” section. Bootstrap values after 1000 re-samplings (16S rRNA gene sequences) and 500 re-samplings (MLSA) are given at the nodes (in %). The outgroups consist of three 16S rRNA genes from the PVC superphylum (16S rRNA-based tree) or the genome sequences of Gemmata obscuriglobus, Rhodopirellula baltica and Gimesia maris (MLSA-based tree)

Fig. 2.

Fig. 2

Open in a new tab

Similarity values of strain ElPT in relation to species in the family Isosphaeraceae. Methods used: 16S rRNA gene sequence identity (16S), average amino acid identity (AAI), average nucleotide identity (ANI), rpoB gene identity (1200 bp fragment) and percentage of conserved proteins (POCP)

Morphological and physiological analyses

Basic features of strain ElPT comprising cell morphology, growth and mechanism of cell division are summarised in Table 1 and compared to T. sociabilis, Isosphaera pallida, Tundrisphaera lichenicola, Singulisphaera acidiphila, Paludisphaera borealis and Aquisphaera giovannonii (Bondoso et al. 2011; Giovannoni et al. 1987; Kovaleva et al. 2019; Kulichevskaya et al. 2008, 2016, 2017). Morphological features of ElPT cells harvested during the exponential growth phase were analysed using phase contrast and scanning electron microscopy (Fig. 3). Strain ElPT forms spherical cells with a typical diameter of 1.4–2.0 µm (Fig. 3a, c), which occur either as single cells or form smaller aggregates of 25–40 cells. Cells divide by budding with the bud having the same shape as the mother cell (Fig. 3a). Cell size and shape of ElPT are comparable to the type species of known genera in the family Isosphaeraceae, with the exception of I. pallida, which forms cells that are considerably larger. All seven compared strains follow the same mode of division and contain crateriform structures on the entire cell surface (no data available for T. sociabilis). The colonies of ElPT have a pink pigmentation, suggesting the production of carotenoids. The colour is similar to the species chosen for comparison, with the exception of S. acidiphila and the closely related T. sociabilis, which lack pigmentation (Table 1). Once isolated, colonies of strain ElPT were observed to grow at the plastic boundary of the Petri dish, only half connected to the agar surface. This tendency to stick to plastic surfaces necessitated the use of glassware for handling of the strain. For example, cells stuck strongly to plastic pipettes, making their transfer difficult. This immediate adsorption towards plastic surfaces might be related to the extracellular matrix abundantly produced by strain ElPT (Fig. 3e). The strain was determined to be non-motile as are the other reference species, except I. pallida, which displays phototactic gliding motility (Giovannoni et al. 1987).

Table 1.

Phenotypic and genotypic features of strain ElPT compared to closely related strains. The genome analysis is based on GenBank accession numbers for strain ElPT (CP036426–CP036431), Tautonia sociabilis (GCA_003977685.1), Isosphaera pallida (CP002353–CP002354), Singulisphaera acidiphila (CP003364–CP003367), Paludisphaera borealis (CP019082–CP019084) and Aquisphaera giovannonii (CP042997–CP042999). The genome of Tundrisphaera lichenicola has not been sequenced yet

Feature ElPT Tautonia sociabilis
GM2012T 		Isosphaera pallida
IS1BT 		Tundrisphaera lichenicola
P12T 		Singulisphaera acidiphila
MOB10T 		Paludisphaera borealis
PX4T 		Aquisphaera giovannonii
OJF2T
Phenotypic characteristics
Shape Spherical Spherical Spherical Spherical Spherical Spherical Spherical
Diameter (µm) 1.7 ± 0.3 1.7–2.9 2.5–3.0 2.2–3.0 1.6–2.6 1.5–2.5 1.6–2.0
Colour Pink White Pink Pink White Bright pink Pink
Relation to oxygen Aerobic Strictly aerobic Strictly aerobic Strictly aerobic Strictly aerobic Aerobic Strictly aerobic
Temperature range (optimum) (°C) 10–33 (30) 37–46 (42) 34–55 (41) 4–28 (15–22) 4–33 (20–26) 6–30 (15–25) 10–35 (30)
pH range (optimum) 6–0-8.5 (7.5) 5.5–9.0 (7.5) 7.8–8.8 4.5–6.8 (5.5–6.0) 4.2–7.5 (5.0–6.2) 3.5–6.5 (5.0.-5.5) 6.5–9.5 (7.5–8.5)
Division Budding Budding Budding Budding Budding Budding Budding
Dimorphic life cycle n.o. n.d. n.d. n.d. n.d. n.d. n.d.
Motility No No Yes, phototactic gliding No No No No
Crateriform structures Ubiquitous n.d. Ubiquitous Ubiquitous Ubiquitous Ubiquitous Ubiquitous
Fimbriae Yes n.d. Yes n.d. n.d. n.d. Yes
Capsule Yes n.d. No n.d. Yes n.d. Yes
Stalk n.o. n.d. n.d. No No n.d. n.d.
Holdfast structure n.o. n.d. No Yes Yes Yes n.d.
Genomic characteristics
Genome size (bp) 9,395,224 6,760,005 5,529,304 n.d. 9,755,686 7,651,896 10,526,296
Plasmids 5 n.d. 1 n.d. 3 2 2
G + C (%) 71.1 ± 0.8 70.1 62.5 ± 3.2 61.2–62.2 62.2 ± 2.3 66.3 ± 4.1 70.8 ± 0.5
Coding density (%) 84.7 85.0 84.7 n.d. 83.5 86.1 85.7
Completeness (%) 98.28 98.28 98.28 n.d. 98.28 96.55 96.55
Contamination (%) 5.17 3.45 0 n.d. 6.90 3.45 5.17
Total genes 7707 5183 3828 n.d. 7689 5961 7953
Genes/Mb 820 767 692 n.d. 788 779 756
Giant genes 0 0 0 n.d. 1 0 1
All protein-coding genes 7556 5084 3761 n.d. 7540 5855 7835
Protein-coding genes/Mb 804 752 680 n.d. 773 765 744
Hypothetical proteins 3399 3175 1821 n.d. 4316 3154 3328
tRNAs 100 84 51 n.d. 81 83 107
16S rRNA genes 3 1 3 n.d. 8 3 3
Open in a new tab

n.o. not observed, n.d. not determined

Fig. 3.

Fig. 3

Open in a new tab

Microscopy images and cell size plot of strain ElPT. The mode of cell division (a) and a general overview of the cell morphology (b, d, e) is shown. Cells tend to form aggregates surrounded by an extracellular matrix (d + e). The scale bar is 1 µm. For determination of the cell size (c) at least 100 representative cells were counted manually or by using a semi-automated object count tool

In M1H NAG ASW medium, strain ElPT was able to grow over a temperature range of 10–33 °C and a pH range of 6.0–8.5 (Fig. 4). Strain ElPT was found to be aerobic, heterotrophic, mesophilic and neutrophilic. Optimal growth was observed at 30 °C and pH 7.5, which led to a maximal growth rate of 0.024 h−1, corresponding to a generation time of 29 h (Fig. 4). The family Isosphaeraceae appears to be heterogeneous regarding temperature and pH preferences. S. acidiphila, T. lichenicola and P. borealis favour lower temperatures (15–26 °C) compared to strain ElPT (30 °C), whereas I. pallida and T. sociabilis are thermophiles with optimal growth at 41–42 °C and a temperature range allowing growth up to 55 °C (Table 1). With regard to pH, I. pallida and A. giovannonii are adapted to slightly alkaline growth conditions (pH 8–9), whereas S. acidiphila, T. lichenicola and P. borealis require more acidic environments (pH 5–6). Strain ElPT and T. sociabilis grow optimally under neutral conditions (pH 7–7.5). These differences likely reflect the different natural habitats from which the strains were isolated. I. pallida was isolated from a hot spring, explaining the preference for higher temperatures, while e.g. S. acidiphila was isolated from a Sphagnum peat moss, which are typically found in nutrient-poor and acidic peat bogs (Giovannoni et al. 1987; Kulichevskaya et al. 2008).

Fig. 4.

Fig. 4

Open in a new tab

Temperature and pH optimum of ElPT. The graphs show the average growth rates obtained from cultivation of the strain in M1H NAG ASW medium in biological triplicates. Cultivations at different temperatures (a) were performed at pH 7.5 and cultivations at different pH values (b) were conducted at 28 °C

Genomic characteristics

The complete genome of strain ElPT has a size of 9.40 Mb, distributed among the chromosome (8.67 Mb) and five plasmids (with sizes of 0.28, 0.14, 0.12, 0.09 and 0.09 Mb). While plasmids are scarce among Planctomycetes, the family Isosphaeraceae is exceptional in that regard (Ivanova et al. 2017). Five strains of this family harbour at least one plasmid (no data available for T. sociabilis), while four plasmids was the current maximum observed in strain SH-PL62 (Ivanova et al. 2017). Strain ElPT maintains five extrachromosomal replicons in parallel, making it a potential resource for future planctomycetal genetic tool development.

The G + C content of strain ElPT is 71.1%. In its genome, 7707 genes were annotated, of which 7556 are putative protein-coding genes. The number of hypothetical proteins is 3399, corresponding to 45% of the total number of putatively annotated proteins. The number of protein-coding genes yields 804 encoded proteins per Mb and a coding density of 84.7%. 100 tRNAs and three copies of the 16S rRNA gene were identified. The genomic characteristics of the compared strains are quite heterogeneous (Table 1). With 5.53 Mb I. pallida has by far the smallest genome, while the genomes of strain ElPT, S. acidiphila and A. giovannonii fall in a size range of 9.4–10.6 Mb. Their G + C content varies from 62 to 71%, with strain ElPT showing the highest G + C content of the compared strains. One giant gene (> 5 kb) was found in S. acidiphila and A. giovannonii, while the other three strains lack giant genes. The genome of T. lichenicola has not been sequenced yet and could thus not be used for comparison.

Genome-based analysis of the primary and secondary metabolism

The genome sequences of species belonging to the family Isosphaeraceae provide important information on their metabolic capabilities. The suggested capability of Planctomycetes to degrade high molecular weight sugars is likely reflected by high numbers of carbohydrate-active enzymes encoded in their genomes, while production of secondary metabolites is often related to interactions with the abiotic and biotic environment, including response to external stress factors. The compared members of the family Isosphaeraceae harbour between 109 and 317 carbohydrate-active enzymes and a clear correlation between the number of enzymes and the genome size was observed (Table 2). Only S. acidiphila slightly deviates from this trend. It has the second largest genome of the compared species, but is only ranked 3rd with regard to the number of carbohydrate-active enzymes. Strain ElPT has a 5% smaller genome, but its number of carbohydrate-active enzymes is around 10% higher. Analysis of the distribution to the different enzyme families shows that glycoside hydrolases and glycosyl transferases account for 80–90% of the total number in all five strains. A. giovannonii has a considerably higher number of enzymes of the glycoside hydrolase family, which is 2.5 times as high as in strain ElPT (second highest number of enzymes of this family) and almost seven times as high as in I. pallida. Whether a higher number of carbohydrate-active enzymes is related to a higher versatility during degradation naturally-occuring polysaccharides remains to be elucidated.

Table 2.

Numbers of carbohydrate-active enzymes and secondary metabolite-associated gene clusters in ElPT in comparison to other species in the family Isosphaeraceae. The analysis is based on GenBank accession numbers for strain ElPT (CP036426–CP036431), Tautonia sociabilis (GCA_003977685.1), Isosphaera pallida (CP002353–CP002354), Singulisphaera acidiphila (CP003364–CP003367), Paludisphaera borealis (CP019082–CP019084) and Aquisphaera giovannonii (CP042997–CP042999)

Feature ElPT Tautonia sociabilis
GM2012T 		Isosphaera pallida
IS1BT 		Singulisphaera acidiphila
MOB10T 		Paludisphaera borealis
PX4T 		Aquisphaera giovannonii
OJF2T
Genome size (Mb) 9.40 6.76 5.53 9.76 7.65 10.53
Carbohydrate-active enzymes
Glycoside Hydrolase Family 59 n.d. 21 49 52 142
Glycosyl Transferase Family 123 n.d. 74 117 86 120
Polysaccharide Lyase Family 3 n.d. 2 1 0 3
Carbohydrate Esterase Family 13 n.d. 5 9 9 17
Carbohydrate-Binding Module Family 16 n.d. 7 14 21 35
Total number 214 n.d. 109 190 168 317
Secondary metabolite-associated clusters
Terpenoid 3 2 3 3 2 2
Type I Polyketide synthase 1 1 1 2 3 2
Type II Polyketide synthase 0 0 0 0 0 0
Type III Polyketide synthase 0 0 1 0 1 1
Non-ribosomal peptide synthetase 0 0 0 0 0 1
Bacteriocin 0 2 0 1 0 1
Resorcinol 0 0 0 0 0 0
Total number 4 5 5 6 6 7
Open in a new tab

To gain a first insight into the secondary metabolism, numbers of genes coding for polyketide synthases (PKSs), non-ribosomal peptide synthetases (NRPSs) and other genes involved in the synthesis of terpenoids, bacteriocins or resorcinol were analysed (Table 2). A correlation between the number of gene clusters and the genome size could also be observed in this case. Five genes/gene clusters were found in species with genome sizes of 5–7 Mb, six in species with 7–10 Mb and seven clusters in A. giovannonii with > 10 Mb genome size. Strain ElPT is an exception to this trend since only four clusters were observed, although the strain has the second largest genome of those compared. All six strains harbour 2–3 genes putatively involved in terpenoid biosynthesis. Genes coding for phytoene synthase isoenzymes (CrtB; catalysing the initial step during carotenoid biosynthesis) were identified in the pink-pigmented strains (see Table 1), however, genes in T. sociabilis and S. acidiphila might well code for closely related squalene synthases. Since the pathway for carotenoid biosynthesis in Planctomycetes has not been discovered yet, additional conclusions cannot be drawn from the genome sequence at this stage. At least one type I PKS-encoding gene is present in all six strains, while three of the strains also harbour a putative type III PKS gene. Type II PKSs were not observed in the compared strains. Two of the strains appear to be capable of bacteriocin production, while a single NRPS-encoding gene was observed in A. giovannonii. The six species may harbour additional gene clusters involved in the production of small molecules, these, however, might have escaped the in silico prediction by the AntiSMASH tool.

Taken together, comparison of morphological, physiological and genomic features in the heterogeneous family Isosphaeraceae supports the results of the phylogenetic analysis, which leads us to the conclusion that strain ElPT represents a novel species in the genus Tautonia. Thus, we propose the name Tautonia plasticadhaerens for this species, represented by the type strain ElPT (DSM 101012T = LMG 29141T).

Emended genus description of Tautonia Kovaleva et al. (2019)

The description of the genus is as previously published (Kovaleva et al. 2019), with the following modification: species of this genus are mesophilic or thermotolerant.

Tautonia plasticadhaerens sp. nov.

Plas.tic.ad.hae'rens. N.L. neut. n. plasticum plastic; L. pres. part. adhaerens adhering, sticking to; N.L. part. adj. plasticadhaerens attaching to plastic, due to the tendency of the type strain to attach strongly to plastic surfaces.

Cells are spherical (diameter 1.7 ± 0.3 µm), occur as single cells or small aggregates and divide by budding. Stalk-free and non-motile cells, which contain crateriform structures covering the entire cell surface. Cells produce an extracellular matrix and strongly attach to plastic surfaces. Colonies are pink. Cells of the type strain grow over a temperature range of 10–33 °C (optimum 30 °C) and at pH 6.0–8.5 (optimum 7.5). The genome of the type strain has a size of 9.40 Mb, which is distributed among the chromosome and five plasmids. The G + C content is 71.1%.

The type strain is ElPT (DSM 101012T = LMG 29141T), isolated from an alga close to Panarea Island in September 2013.

Acknowledgements

Open Access funding provided by Projekt DEAL. Part of this research was funded by the Deutsche Forschungsgemeinschaft Grants KA 4967/1-1 and JO 893/4-1, Grant ALWOP.308 of the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO), SIAM (Soehngen Institute for Anaerobic Microbiology) Grant No. 024002002 and the Radboud Excellence fellowship. We thank Ina Schleicher for skilful technical assistance. Brian Tindall and Regine Fähnrich from the DSMZ as well as the BCCM/LMG Bacteria collection we thank for support during strain deposition. We thank the Scientific Diving Center of the Bergakademie Freiberg, Germany, Thomas Pohl, Peter Hornburger and all participants of the 2013 Panarea Expedition for sampling support.

Author contributions

NK wrote the manuscript and analysed the cultivation data, SW performed the genomic and phylogenetic analysis, AH and MJ isolated the strains and performed the initial cultivation and strain deposition, SHP and CB performed the light microscopic analysis and prepared the LM pictures, MSMJ contributed to text preparation and revised the manuscript, MR performed the electron microscopic analysis and prepared the SEM pictures, CJ supervised AH and the study. All authors read and approved the final version of the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with animals performed by any of the authors.

Footnotes

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

References

  1. Bengtsson MM, Øvreås L. Planctomycetes dominate biofilms on surfaces of the kelp Laminaria hyperborea. BMC Microbiol. 2010;10:261. doi: 10.1186/1471-2180-10-261. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, Suarez Duran HG, de Los Santos EL, Kim HU, Nave M. antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 2017;45:W36–W41. doi: 10.1093/nar/gkx319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Boedeker C, Schuler M, Reintjes G, Jeske O, van Teeseling MC, Jogler M, Rast P, Borchert D, Devos DP, Kucklick M, Schaffer M, Kolter R, van Niftrik L, Engelmann S, Amann R, Rohde M, Engelhardt H, Jogler C. Determining the bacterial cell biology of Planctomycetes. Nat Commun. 2017;8:14853. doi: 10.1038/ncomms14853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Boersma AS, Kallscheuer N, Wiegand S, Rast P, Peeters SH, Mesman RJ, Heuer A, Boedeker C, Jetten MS, Rohde M, Jogler M, Jogler C. Alienimonas californiensis gen. nov. sp. Nov., a novel Planctomycete isolated from the kelp forest in Monterey Bay. Antonie van Leeuwenhoek. 2019 doi: 10.1007/s10482-019-01367-4. [DOI] [PubMed] [Google Scholar]
  5. Bondoso J, Albuquerque L, Nobre MF, Lobo-da-Cunha A, da Costa MS, Lage OM. Aquisphaera giovannonii gen. nov., sp. nov., a planctomycete isolated from a freshwater aquarium. Int J Syst Evol Microbiol. 2011;61:2844–2850. doi: 10.1099/ijs.0.027474-0. [DOI] [PubMed] [Google Scholar]
  6. Bondoso J, Harder J, Lage OM. rpoB gene as a novel molecular marker to infer phylogeny in Planctomycetales. Antonie Van Leeuwenhoek. 2013;104:477–488. doi: 10.1007/s10482-013-9980-7. [DOI] [PubMed] [Google Scholar]
  7. Bondoso J, Balague V, Gasol JM, Lage OM. Community composition of the Planctomycetes associated with different macroalgae. FEMS Microbiol Ecol. 2014;88:445–456. doi: 10.1111/1574-6941.12258. [DOI] [PubMed] [Google Scholar]
  8. Bondoso J, Godoy-Vitorino F, Balague V, Gasol JM, Harder J, Lage OM. Epiphytic Planctomycetes communities associated with three main groups of macroalgae. FEMS Microbiol Ecol. 2017;93:fiw255. doi: 10.1093/femsec/fiw255. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cayrou C, Raoult D, Drancourt M. Broad-spectrum antibiotic resistance of Planctomycetes organisms determined by Etest. J Antimicrob Chemother. 2010;65:2119–2122. doi: 10.1093/jac/dkq290. [DOI] [PubMed] [Google Scholar]
  10. Dedysh SN, Kulichevskaya IS, Beletsky AV, Ivanova AA, Rijpstra WIC, Damsté JSS, Mardanov AV, Ravin NV. Lacipirellula parvula gen. nov., sp. nov., representing a lineage of planctomycetes widespread in low-oxygen habitats, description of the family Lacipirellulaceae fam. nov. and proposal of the orders Pirellulales ord. nov., Gemmatales ord. nov. and Isosphaerales ord. nov. Syst Appl Microbiol. 2019;43:126050. doi: 10.1016/j.syapm.2019.126050. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Devos DP. PVC bacteria: variation of, but not exception to, the Gram-negative cell plan. Trends Microbiol. 2014;22:14–20. doi: 10.1016/j.tim.2013.10.008. [DOI] [PubMed] [Google Scholar]
  12. Frank O, Michael V, Pauker O, Boedeker C, Jogler C, Rohde M, Petersen J. Plasmid curing and the loss of grip - The 65-kb replicon of Phaeobacter inhibens DSM 17395 is required for biofilm formation, motility and the colonization of marine algae. Syst Appl Microbiol. 2014;38:120–127. doi: 10.1016/j.syapm.2014.12.001. [DOI] [PubMed] [Google Scholar]
  13. Giovannoni S, Schabtach E, Castenholz R. Isosphaera pallida, gen. and comb. nov., a gliding, budding eubacterium from hot springs. Arch Microbiol. 1987;147:276–284. doi: 10.1128/jb.169.6.2702-2707.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Godinho O, Calisto R, Ovreas L, Quinteira S, Lage OM. Antibiotic susceptibility of marine Planctomycetes. Antonie Van Leeuwenhoek. 2019;112:1273–1280. doi: 10.1007/s10482-019-01259-7. [DOI] [PubMed] [Google Scholar]
  15. Ivanova AA, Naumoff DG, Miroshnikov KK, Liesack W, Dedysh SN. Comparative genomics of four Isosphaeraceae planctomycetes: a common pool of plasmids and glycoside hydrolase genes shared by Paludisphaera borealis PX4T, Isosphaera pallida IS1BT, Singulisphaera acidiphila DSM 18658T, and strain SH-PL62. Front Microbiol. 2017;8:412. doi: 10.3389/fmicb.2017.00412. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Jeske O, Jogler M, Petersen J, Sikorski J, Jogler C. From genome mining to phenotypic microarrays: Planctomycetes as source for novel bioactive molecules. Antonie Van Leeuwenhoek. 2013;104:551–567. doi: 10.1007/s10482-013-0007-1. [DOI] [PubMed] [Google Scholar]
  17. Jeske O, Schüler M, Schumann P, Schneider A, Boedeker C, Jogler M, Bollschweiler D, Rohde M, Mayer C, Engelhardt H, Spring S, Jogler C. Planctomycetes do possess a peptidoglycan cell wall. Nat Commun. 2015;6:7116. doi: 10.1038/ncomms8116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Jogler M, Jogler C. Towards the development of genetic tools for Planctomycetes. In: Fuerst JA, editor. Planctomycetes: cell structure, origins and biology. Berlin: Springer; 2013. pp. 141–164. [Google Scholar]
  19. Jogler C, Glöckner FO, Kolter R. Characterization of Planctomyces limnophilus and development of genetic tools for its manipulation establish it as a model species for the phylum Planctomycetes. Appl Environ Microbiol. 2011;77:5826–5829. doi: 10.1128/AEM.05132-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Jogler C, Waldmann J, Huang X, Jogler M, Glöckner FO, Mascher T, Kolter R. Identification of proteins likely to be involved in morphogenesis, cell division, and signal transduction in Planctomycetes by comparative genomics. J Bacteriol. 2012;194:6419–6430. doi: 10.1128/JB.01325-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kallscheuer N, Jogler M, Wiegand S, Peeters SH, Heuer A, Boedeker C, Jetten MS, Rohde M, Jogler C. Rubinisphaera italica sp. Nov. isolated from a hydrothermal area in the Tyrrhenian Sea close to the volcanic island Panarea. Antonie van Leeuwenhoek. 2019 doi: 10.1007/s10482-019-01329-w. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Kallscheuer N, Jogler M, Wiegand S, Peeters SH, Heuer A, Boedeker C, Jetten MS, Rohde M, Jogler C. Three novel Rubripirellula species isolated from plastic particles submerged in the Baltic Sea and the estuary of the river Warnow in northern Germany. Antonie Van Leeuwenhoek. 2019 doi: 10.1007/s10482-019-01368-3. [DOI] [PubMed] [Google Scholar]
  23. Kallscheuer N, Moreira C, Airs R, Llewellyn CA, Wiegand S, Jogler C, Lage OM. Pink-and orange-pigmented Planctomycetes produce saproxanthin-type carotenoids including a rare C45 carotenoid. Environ Microbiol Rep. 2019;11:741–748. doi: 10.1111/1758-2229.12796. [DOI] [PubMed] [Google Scholar]
  24. Kallscheuer N, Wiegand S, Peeters SH, Jogler M, Boedeker C, Heuer A, Rast P, Jetten MS, Rohde M, Jogler C. Description of three bacterial strains belonging to the new genus Novipirellula gen. nov., reclassificiation of Rhodopirellula rosea and Rhodopirellula caenicola and readjustment of the genus threshold of the phylogenetic marker rpoB for Planctomycetaceae. Antonie van Leeuwenhoek. 2019 doi: 10.1007/s10482-019-01374-5. [DOI] [PubMed] [Google Scholar]
  25. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014;64:346–351. doi: 10.1099/ijs.0.059774-0. [DOI] [PubMed] [Google Scholar]
  26. Kohn T, Wiegand S, Boedeker C, Rast P, Heuer A, Schüler M, Rohde C, Müller R-W, Brümmer F, Rohde M, Engelhardt H, Jogler M, Jogler C. Planctopirus ephydatiae, a novel Planctomycete isolated a freshwater sponge. Syst Appl Microbiol. 2019;43:126022. doi: 10.1016/j.syapm.2019.126022. [DOI] [PubMed] [Google Scholar]
  27. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol. 2005;187:6258–6264. doi: 10.1128/JB.187.18.6258-6264.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Kovaleva OL, Elcheninov AG, Toshchakov SV, Novikov AA, Bonch-Osmolovskaya EA, Kublanov IV. Tautonia sociabilis gen. nov., sp. nov., a novel thermotolerant planctomycete, isolated from a 4000 m deep subterranean habitat. Int J Syst Evol Microbiol. 2019;69:2299–2304. doi: 10.1099/ijsem.0.003467. [DOI] [PubMed] [Google Scholar]
  29. Kulichevskaya IS, Ivanova AO, Baulina OI, Bodelier PL, Damste JSS, Dedysh SN. Singulisphaera acidiphila gen. nov., sp. nov., a non-filamentous, Isosphaera-like planctomycete from acidic northern wetlands. Int J Syst Evol Microbiol. 2008;58:1186–1193. doi: 10.1099/ijs.0.65593-0. [DOI] [PubMed] [Google Scholar]
  30. Kulichevskaya IS, Ivanova AA, Suzina NE, Rijpstra WIC, Damste JSS, Dedysh SN. Paludisphaera borealis gen. nov., sp. nov., a hydrolytic planctomycete from northern wetlands, and proposal of Isosphaeraceae fam. nov. Int J Syst Evol Microbiol. 2016;66:837–844. doi: 10.1099/ijsem.0.000799. [DOI] [PubMed] [Google Scholar]
  31. Kulichevskaya IS, Ivanova AA, Detkova EN, Rijpstra WIC, Damsté JSS, Dedysh SN. Tundrisphaera lichenicola gen. nov., sp. nov., a psychrotolerant representative of the family Isosphaeraceae from lichen-dominated tundra soils. Int J Syst Evol Microbiol. 2017;67:3583–3589. doi: 10.1099/ijsem.0.002172. [DOI] [PubMed] [Google Scholar]
  32. Kürzinger V (2019) Determination and differentiation of the hydrothermal precipitates of Panarea, Italy, FOG-Freiberg Online Geoscience, Nr. 54
  33. Lachnit T, Fischer M, Kunzel S, Baines JF, Harder T. Compounds associated with algal surfaces mediate epiphytic colonization of the marine macroalga Fucus vesiculosus. FEMS Microbiol Ecol. 2013;84:411–420. doi: 10.1111/1574-6941.12071. [DOI] [PubMed] [Google Scholar]
  34. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol. 2016;66:1100–1103. doi: 10.1099/ijsem.0.000760. [DOI] [PubMed] [Google Scholar]
  35. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:D490–D495. doi: 10.1093/nar/gkt1178. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Panter F, Garcia R, Thewes A, Zaburannyi N, Bunk B, Overmann J, Gutierrez MV, Krug D, Müller R. Production of a dibrominated aromatic secondary metabolite by a Planctomycete implies complex interaction with a macroalgal host. ACS Chem Biol. 2019;14:2713–2719. doi: 10.1021/acschembio.9b00641. [DOI] [PubMed] [Google Scholar]
  37. Peeters SH, Wiegand S, Kallscheuer N, Jogler M, Heuer A, Jetten MS, Rast P, Boedeker C, Rohde M, Jogler C. Three marine strains constitute the novel genus and species Crateriforma conspicua in the phylum Planctomycetes. Antonie Van Leeuwenhoek. 2020 doi: 10.1007/s10482-019-01375-4. [DOI] [PubMed] [Google Scholar]
  38. Pilhofer M, Rappl K, Eckl C, Bauer AP, Ludwig W, Schleifer KH, Petroni G. Characterization and evolution of cell division and cell wall synthesis genes in the bacterial phyla Verrucomicrobia,Lentisphaerae, Chlamydiae, and Planctomycetes and phylogenetic comparison with rRNA genes. J Bacteriol. 2008;190:3192–3202. doi: 10.1128/JB.01797-07. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C, Zhou J, Oren A, Zhang Y-Z. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol. 2014;196:2210–2215. doi: 10.1128/JB.01688-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Rast P, Glockner I, Boedeker C, Jeske O, Wiegand S, Reinhardt R, Schumann P, Rohde M, Spring S, Glockner FO, Jogler C, Jogler M. Three novel species with peptidoglycan cell walls form the new genus Lacunisphaera gen. nov. in the family Opitutaceae of the Verrucomicrobial subdivision 4. Front Microbiol. 2017;8:202. doi: 10.3389/fmicb.2017.00202. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Ravin NV, Rakitin AL, Ivanova AA, Beletsky AV, Kulichevskaya IS, Mardanov AV, Dedysh SN. Genome analysis of Fimbriiglobus ruber SP5T, a planctomycete with confirmed chitinolytic capability. Appl Environ Microbiol. 2018;84:e02645–e2717. doi: 10.1128/AEM.02645-17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Rensink S, Wiegand S, Kallscheuer N, Rast P, Peeters SH, Heuer A, Boedeker C, Jetten MS, Rohde M, Jogler M, Jogler C. Description of the novel planctomycetal genus Bremerella, containing Bremerella volcania sp. Nov., isolated from an active volcanic site, and reclassification of Blastopirellula cremea as Bremerella cremea comb. nov. Antonie van Leeuwenhoek. 2020 doi: 10.1007/s10482-019-01378-1. [DOI] [PubMed] [Google Scholar]
  43. Rivas-Marin E, Canosa I, Santero E, Devos DP. Development of genetic tools for the manipulation of the Planctomycetes. Front Microbiol. 2016;7:914. doi: 10.3389/fmicb.2016.00914. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints. 2016;4:e1900v1. [Google Scholar]
  45. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7:539. doi: 10.1038/msb.2011.75. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Spring S, Bunk B, Spröer C, Schumann P, Rohde M, Tindall BJ, Klenk H-P. Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum. ISME J. 2016;10:2801. doi: 10.1038/ismej.2016.84. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today. 2006;33:152–155. [Google Scholar]
  48. van Teeseling MC, Mesman RJ, Kuru E, Espaillat A, Cava F, Brun YV, VanNieuwenhze MS, Kartal B, van Niftrik L. Anammox Planctomycetes have a peptidoglycan cell wall. Nat Commun. 2015;6:6878. doi: 10.1038/ncomms7878. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Vollmers J, Frentrup M, Rast P, Jogler C, Kaster AK. Untangling genomes of novel Planctomycetal and Verrucomicrobial species from Monterey Bay Kelp Forest metagenomes by refined binning. Front Microbiol. 2017;8:472. doi: 10.3389/fmicb.2017.00472. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Wagner M, Horn M. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol. 2006;17:241–249. doi: 10.1016/j.copbio.2006.05.005. [DOI] [PubMed] [Google Scholar]
  51. Wiegand S, Jogler M, Jogler C. On the maverick Planctomycetes. FEMS Microbiol Rev. 2018;42:739–760. doi: 10.1093/femsre/fuy029. [DOI] [PubMed] [Google Scholar]
  52. Wiegand S, Jogler M, Boedeker C, Pinto D, Vollmers J, Rivas-Marín E, Kohn T, Peeters SH, Heuer A, Rast P, Oberbeckmann S, Bunk B, Jeske O, Meyerdierks A, Storesund JE, Kallscheuer N, Lücker S, Lage OM, Pohl T, Merkel BJ, Hornburger P, Müller R-W, Brümmer F, Labrenz M, Spormann AM, Op den Camp HJM, Overmann J, Amann R, Jetten MSM, Mascher T, Medema MH, Devos DP, Kaster A-K, Øvreås L, Rohde M, Galperin MY, Jogler C. Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology. Nat Microbiol. 2020;5:126–140. doi: 10.1038/s41564-019-0588-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, Whitman WB, Euzeby J, Amann R, Rossello-Mora R. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol. 2014;12:635–645. doi: 10.1038/nrmicro3330. [DOI] [PubMed] [Google Scholar]

Articles from Antonie Van Leeuwenhoek are provided here courtesy of Springer

RESOURCES