REVIEWS

Beyond the bacterium: planctomycetes

challenge our concepts of microbial
structure and function
John A. Fuerst and Evgeny Sagulenko
Abstract | Planctomycetes form a distinct phylum of the domain Bacteria and possess
unusual features such as intracellular compartmentalization and a lack of peptidoglycan in
their cell walls. Remarkably, cells of the genus Gemmata even contain a membrane-bound
nucleoid analogous to the eukaryotic nucleus. Moreover, the so-called ‘anammox’
planctomycetes have a unique anaerobic, autotrophic metabolism that includes the ability
to oxidize ammonium; this process is dependent on a characteristic membrane-bound cell
compartment called the anammoxosome, which might be a functional analogue of the
eukaryotic mitochondrion. The compartmentalization of planctomycetes challenges our
hypotheses regarding the origins of eukaryotic organelles. Furthermore, the recent discovery
of both an endocytosis-like ability and proteins homologous to eukaryotic clathrin in a
planctomycete marks this phylum as one to watch for future research on the origin and
evolution of the eukaryotic cell.

Nucleoid
The region of the bacterial cell
that contains the genomic
DNA, usually seen in thin
sections as a fibrillar region;
in electron micrographs of
cryosubstituted Escherichia
coli cell sections, the nucleoid
seems to occupy much of the
cell, whereas it forms a highly
condensed fibrillar structure in
planctomycetes.
School of Chemistry and
Molecular Biosciences,
The University of Queensland,
St Lucia, Brisbane,
Queensland 4072, Australia.
Correspondence to J.A.F. 
e-mail: j.fuerst@uq.edu.au
doi:10.1038/nrmicro2578
Planctomycetes are all around us — ubiquitous in soil1,
fresh water 2–4, the oceans and oceanic abyssal sedi-
ments5,6, they live in places as far removed and extreme
as the Atacama Desert in South America7, the oxygen-
minimum zones of the Atlantic Ocean’s Benguela
Current off the African coast 8, wild-gorilla faeces9 and
palaeolithic cave paintings10. These microorganisms are
a largely unexplored group that represents an excellent
example of the value of studying bacteria other than
‘classical’ models such as Escherichia coli. The group
includes species that challenge our fundamental notions
of the bacterial cell plan and may help us understand
how the complex internal structure of our own eukaryo-
tic cells originated billions of years ago. Other species
have key roles in the global nitrogen cycle and could
potentially be used in new processes to treat nitrogen-
polluted waste, soak up atmospheric carbon dioxide and
generate energy from sewage. Still other species produce
enzymes that could form the basis for new stereoselective
industrial chemistry.  many ‘mainstream’ chemoheterotrophs. Representatives
In this Review, we summarize recent developments in
our understanding of planctomycete cell structure and cell
biology in relation to the functions of the characteristic
planctomycete cell compartments. We also discuss insights
from genomic and proteomic analyses of these micro­
organisms and, finally, the implications of the findings
from planctomycete research for our understanding of the
origin and evolution of eukaryotes.
Planctomycete unity and diversity
Planctomycetes possess distinctive phenotypic features
that are highly unusual among bacteria. These include the
absence of peptidoglycan in their protein cell walls and,
as discussed below, the compartmentalization of cells by
means of internal membranes, including the formation
of the membrane-bound nucleoid3 (FIG. 1). Furthermore,
almost all planctomycetes reproduce by a budding process,
with the exception of one divergent marine genus that uses
binary fission11. As a result of their lack of peptido­glycan,
planctomycetes are inherently resistant to anti­biotics
that inhibit cell wall synthesis, such as the β‑lactams and
vancomycin12, providing a useful tool for the isolation
of these organisms in pure culture.
Planctomycetes include some species with remark-
ably unusual physiology, although they also include
of several genera have been successfully isolated in pure
culture from a variety of aquatic and terrestrial envi-
ronments2,11,13–18, but other planctomycetes have been
studied using only culture-independent methods or
enrichment cultures (TABLE 1). In particular, no member
of the ‘anammox’ planctomycetes, which include both

NATURE REVIEWS | MICROBIOLOGY VOLUME 9 | JUNE 2011 | 403

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REVIEWS
Intracytoplasmic
membrane
Pirellulosome Paryphoplasm
Ribosome
Cytoplasmic Cell
Nucleoid membrane wall
Pirellulosome
Paryphoplasm Paryphoplasm
Figure 1 | An idealized planctomycete in the process of cell division. The unusual
compartmentalized cell structure of the planctomycetes is Nature
shown,Reviews
detailing| Microbiology
the protein
cell wall, the cytoplasmic membrane lipid bilayer and the intracytoplasmic membrane
lipid bilayer in relation to the ribosome-free paryphoplasm and the ribosome-containing
pirellulosome that contains condensed nucleoid DNA. The exact mechanism of bud
formation and membrane transfer into the bud has not been determined in the simplest
type of planctomycete shown here (but see REF. 72 for data relating to the more complex
Gemmata obscuriglobus).
fresh wastewater 19,20 and marine21 species, has been iso-
lated in pure culture to date; these microorganisms are
anaerobic and chemoautotrophic, and oxidize ammo-
nium to dinitrogen. For this reason, they are important
for the global nitrogen cycle and for remediation of
ammonia-rich wastewater 22.
It is remarkable that some planctomycetes can synthe-
size sterols23, an ability that is typical of eukaryotes and
unusual among bacteria. In particular, Gemmata spp.
can synthesize C30 sterols, such as lanosterol, which are
found in eukaryotes and in only two other groups of
bacteria: methylotrophic proteobacteria (for example,
Methylococcus capsulatus) and myxobacteria. Sterol
synthesis in Gemmata spp. has been proposed to be a
remnant of an ancient sterol biosynthesis pathway, but
the alternative view of lateral gene transfer has also been
suggested24. It has been speculated that sterols might
regulate membrane fluidity in the characteristic internal
membranes of planctomycetes.
Another unusual metabolic feature of plancto­mycetes
is that they possess genes which encode enzymes for
C1 transfer. These enzymes had previously been found
in only methane-generating archaea and a methane-
Anammox oxidizing group of proteobacteria, in which they have a
Anaerobic ammonium role in the metabolism of compounds with one carbon
oxidation, a process performed atom. Although a possible role in formaldehyde detoxifi-
by some species of cation has been proposed for these enzymes, in plancto­
planctomycetes, whereby
ammonium is oxidized to
mycetes there is no correlation between the presence of
dinitrogen using nitrite as an the genes that encode these enzymes and any known
electron acceptor via ability to use or produce C1 compounds5,25, and a func-
intermediates, including toxic tion in adaptation to suboxic conditions in the ocean
hydrazine.
has also been suggested5. There is currently some debate
C1 transfer concerning whether these genes are remnants from
The process by which a ancient methano­genic or methyl­trophic ancestors or
compound containing only one whether they were horizontally acquired from either
carbon atom (a C1 compound; archaea or other bacteria26.
such as methane, methylamine,
formate and formaldehyde) is
The question of the taxonomic position of plancto­
enzymatically transformed into mycetes is closely intertwined with the issue of their
another C1 compound. diversity. The planctomycetes were originally separated
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© 2011 Macmillan Publishers Limited. All rights reserved
as a division of the ‘eubacteria’ on the basis of oligo­
nucleotide catalogues27, and more recent analyses using
concatenated protein-coding gene sets and genomes
have confirmed that these organisms form a distinct
bacterial phylum28,29. It has been proposed that plancto-
mycetes should be included in new coarse-level bacterial
clades, such as Negibacteria (which encompass Gram-
negative bacteria) or Gracilicutes (which include the
proteo­bacteria, spirochaetes and sphingobacteria), but
these classifications do not take into account the distinct
protein nature of the planctomycete cell walls30,31, which
lack peptidoglycan and its components (such as muramic
acid and diaminopimelic acid), in contrast to the cell
walls of other members of the proposed clades32,33. It
should be noted, however, that some planctomycetes
possess 3‑hydroxy fatty acids34, which are typically found
in the cell walls of Gram-negative bacteria. Furthermore,
the genomes of some planctomycetes include genes with
similarity to those encoding enzymes for lipid A synthe-
sis in Gram-negative bacteria, although the synthesis of
O polysaccharide (also known as the O antigen) chains
and a true outer membrane lipopolysaccharide are not
predicted by these genomic analyses35.
Some phylogenetic studies using the analysis of either
conserved positions in ribosomal RNA sequences36 or
whole proteomes29 suggest that the Planctomycetes
may be the deepest branch among the phyla of the
domain Bacteria (FIG. 2a). The phylum Planctomycetes
has been grouped with other bacterial phyla to form the
Planctomycetes–Verrucomicrobia–Chlamydiae (PVC)
superphylum, which includes the phyla Verrucomicrobia
(containing soil bacteria), Lentisphaerae (containing
marine organisms), ‘Candidatus Poribacteria’ (con-
taining symbionts of marine sponges) and Chlamydiae
(containing human pathogens), and the candidate divi-
sion OP3 (containing species found in anoxic habitats
such as rice paddy soil)37,38; FIG. 2b shows a tree based on
23S rRNA to illustrate the PVC clade. It is noteworthy
that verrucomicrobia and some poribacteria and lenti­
sphaerae seem to be compartmentalized by internal
membranes similarly to the simplest of planctomycete
cell plans39,40. Moreover, genes encoding putative sterol-
synthesizing enzymes are present in the genome of a
‘Candidatus Poribacteria’ member that was sequenced
by single-cell techniques41.
A strong relationship between planctomycetes
and chlamydiae was indicated by phylogenetic analy-
ses using concatenated sequences from 49 proteins
and from 5S–16S–23S rRNA28. Planctomycetes also
possess a homologue of the 60 kD, cysteine-rich
outer membrane protein 2 (Omp2; also known as
OmcB) of chlamydiae, which is interesting in light
of the cysteine-rich wall proteins of planctomycetes,
but also because Omp2 is a target of the immune
response in chlamydial infections28,42. The close rela-
tionship between members of the two phyla is further
supported by the absence of peptidoglycan in their
cell walls. However, it should be noted that chlamy-
dial genomes have genes for an apparently complete
peptidoglycan biosynthesis pathway. The genome of
the anammox planctomycete ‘Candidatus Kuenenia
 REVIEWS

Table 1 | Summary of planctomycete diversity Planctomycete ecology

Species
Mesophilic heterotrophic aerobes
Planctomyces bekefii
Planctomyces guttaeformis
Planctomyces stranskae
Planctomyces brasiliensis
Planctomyces limnophilus
Planctomyces maris
Aquisphaera giovannonii
Blastopirellula marina
Gemmata obscuriglobus
Pirellula staleyi
Rhodopirellula baltica
Moderate thermophilic, heterotrophic aerobe, obligate oligotroph,
with gliding phototactic motility
Isosphaera pallida
Acidophilic heterotrophic aerobes
Schlesneria paludicola
Singulisphaera acidiphila
Zarvarzinella formosa
Heterotrophic facultative anaerobe
Phycisphaera mikurensis
Anammox species (autotrophic anaerobes that oxidize ammonia to dinitrogen)
‘Candidatus Anammoxoglobus
propionicus’*
‘Candidatus Brocadia fulgida’
‘Candidatus Kuenenia
stuttgartiensis’
‘Candidatus Scalindua arabica’
‘Candidatus Scalindua brodae’
‘Candidatus Scalindua sorokinii’
‘Candidatus Scalindua wagneri’
‘Candidatus Jettenia asiatica’
*Also capable of oxidizing propionic acid.
Sulphatases
Enzymes that hydrolytically
cleave sulphate esters to yield
inorganic sulphate and an
alcohol.
Habitat
Fresh water (uncultured morphotypes only)
Fresh water (uncultured morphotypes only)
Fresh water (uncultured morphotypes only)
Hypersaline pond
Fresh water
Marine water
Fresh water
Marine water
Fresh water
Fresh water
Marine water (brackish Baltic Sea)
Hot springs
Sphagnum spp.-dominated boreal wetlands
(acid peat bog)
Acid peat bog
Acid peat bog
Marine alga (Porphyra sp.)
Fresh water (nitrogen-rich wastewater)
Fresh water (nitrogen-rich wastewater)
Fresh water (nitrogen-rich wastewater)
Marine oxygen-poor water and fresh water (e.g.
Lake Tanganyika)
Fresh water (wastewater)
Marine oxygen-poor water (e.g. Black Sea)
Fresh water (wastewater)
Fresh water (wastewater)
stuttgartiensis’ contains 19 of the 21 genes that are
required for peptidoglycan synthesis, but other
plancto­mycetes such as Rhodopirellula baltica have
only a few of these 21 genes. It is also noteworthy that
some members of the phylum Verrucomicrobia pos-
sess peptidoglycan, whereas others apparently do not.
Thus, the common ancestor of the PVC superphylum
probably contained genes for a complete peptidogly-
can biosynthesis pathway that were differentially lost
during the evolution of the different PVC members28.
However, even if this ancestor synthesized peptido­
glycan, it is difficult to deduce whether its cell wall
would have been a Gram-negative or a Gram-positive
type, considering the largely proteinaceous cell wall of
present-day planctomycetes.
Planctomycetes are found throughout the environment,
including in marine, freshwater and soil habitats 1–3.
They can be isolated from, for example, the Atacama
Desert, Chile7 (one of the most arid habitats on Earth),
the living stromatolites of Shark Bay, Australia43, and the
alkaline guts of soil-feeding termites44. They can be
present in some habitats in surprisingly high numbers
— for example, 108 cells per ml in intertidal marine sedi-
ments45. Planctomycete sequences are often observed
in many 16S rRNA-based clone libraries derived from
environmental microbial communities such as those of
wastewater and soil1,46. By using selective media with
carbohydrates as carbon and energy sources, some of
these microorganisms can be retrieved in pure culture
as aerobic chemoheterotrophs from a wide range of habi-
tats, including lake water, sea water, soil, landfill waste,
Antarctic lakes, carnivorous plants, the guts of prawns,
and marine sponges2,17,47,48. Furthermore, molecular
studies suggest that planctomycetes may be important
components of detritus particles that drift through ocean
water (‘marine snow’)49 and of the bacterial communities
that are associated with blooms of marine diatoms50.
Remarkably, planctomycetes were recently shown
to dominate the microbial community of biofilms on
surfaces of the large brown kelp seaweed (Laminaria
hyperborea) in sea water off Norway 51. Given that kelps
form dense marine forests that are extremely important
for coastal productivity around the world, the associated
bacteria might also have important roles in this habitat
(for instance, in carbon and nitrogen turnover). It would
be interesting to determine whether the numerous
sulphatases that are apparently encoded in the genomes
of some marine planctomycetes (such as Rhodopirellula
spp.; see below) have any role in the metabolism of the
sulphate polysaccharides (such as fucoidin) that are
produced by kelps.
The anammox planctomycetes are found in both
marine and freshwater habitats and are widely distrib-
uted in vast anoxic zones of the ocean8,52–54. They are
major contributors to the global nitrogen cycle: it has
been estimated that 50% of the nitrogen molecules in the
atmosphere have been generated by these organisms55.
The anammox process is also of great significance for
nitrogen-rich-wastewater remediation technology, and
full-scale anammox plants using this process for treat-
ing municipal wastewater are now in operation56; new
applications of this process may even form the basis for
energy-generating sewage treatment 57.
Some planctomycetes can also be found in thermo­
philic habitats. Isosphaera pallida, which was isolated
from a hot spring, is a moderate thermophile that can
grow at temperatures as high as 55 °C 58; it seems to be a
heterotroph associated with the photosynthetic bacterium
Heliothrix oregonensis 59. Recently, anammox plancto­
mycetes have been reported in high-temperature oil res-
ervoirs with production waters of up to 75 °C 60, as well
as in deep-sea hydrothermal vents at up to 85 °C 61.
Because of their considerable divergence from
members of other bacterial phyla, some plancto­mycetes
may have been missed in metagenomic analyses of

NATURE REVIEWS | MICROBIOLOGY VOLUME 9 | JUNE 2011 | 405

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REVIEWS

Clathrin
A eukaryotic protein that coats
the vesicles formed during
endocytosis.
environmental samples — that is, certain supposedly
universal primers for PCR amplification of bacterial 16S
rRNA genes may not be effective for amplification of
the corresponding planctomycete genes62. New primers
have been designed that seem to have improved specifi-
city for planctomycete 16S rRNA genes63. These issues
should be taken into account in any future studies of
plancto­mycete diversity that use PCR as a first step, and
in the design of probes for planctomycete quantitation
by fluorescence in situ hybridization (FISH).
Planctomycete cell biology
One of the most remarkable features of planctomycetes
is the compartmentalization of their cells by internal
membranes, which define cell regions that are bounded
by either single bilayer membranes or, in some cases,
double membranes composed of two bilayers (FIG. 3).
All known planctomycetes have a characteristic dis-
tinctive cell plan in which the cell is divided into two
major regions: parypho­plasm and pirellulosome15,18,64–66.
The paryphoplasm is a ribosome-free region between
the cytoplasmic membrane and an internal membrane
called the intracytoplasmic membrane (ICM). The
pirellulo­some is an inner region that contains the ribo­
somes and the nucleoid and is enclosed by the ICM. This
compartment was named after its discovery in members
of the genus Pirellula and their relatives64,66,67 (FIG. 3a); it
is also called the riboplasm or ribosome-containing
cytoplasm. It should be noted that the nature of the
paryphoplasm is distinct from that of the periplasm of
Gram-negative proteobacteria: the detection of RNA in
the paryphoplasm of Pirellula and Gemmata spp. (by
RNase–gold immuno­electron microscopy) is evidence
for the cytoplasmic nature of this compartment 64. Thus,
the parypho­plasm is not a type of large periplasm but a
genuine internal cell compartment of cytoplasmic nature
that is distinct from any periplasm that planctomycetes
might also possess between their cytoplasmic mem-
brane and their cell wall. The outermost membrane of
the cell in planctomycetes is hard to visualize by electron
microscopy (EM) because of its close association with
the innermost layer of the cell wall, but it is demon-
strable in thin sections and seems to be a genuine cyto-
plasmic membrane, defined as the bilayer membrane
that encloses all of the cell cytoplasm and is in contact
with that cytoplasm. In the anammox planctomycete
‘Ca. Kuenenia stuttgartiensis’, the outermost membrane
contains ATP synthase, consistent with its postulated
role as an energized cytoplasmic membrane68.
A bacterium with a ‘nucleus’. Gemmata obscuriglobus
displays one of the most unusual internal structures
among bacteria: its nucleoid DNA is surrounded by
an envelope consisting of two closely apposed mem-
branes65,69 (FIG. 3b), forming a nuclear body organelle that,
in turn, lies within the ribosome-filled pirellulosome
bounded by a single ICM. The nuclear body thus forms
a structure that is analogous to the enveloped nucleus
of a eukaryotic cell65. In contrast to the eukaryotic
nucleus, however, the nuclear body contains ribo­
some-like particles. Given that the genome seems to be
Figure 2 | Phylogenetic relationships between ▶
planctomycetes and other organisms. a | A tree of
representatives of the domains Bacteria, Archaea and
Eukarya, constructed by comparing feature frequency
profiles of whole proteomes, and showing a deep-branching
position for planctomycetes relative to other bacterial
phyla. The colouring of branches indicates ‘supraclass’
groups, which are defined by statistical support values of
>82, except for in the Archaea, for which there are three
clear clades according to this analysis. The numbers
indicate the jack-knife monophyly index (%), which is a
measure of statistical support for the branching order
of major groups. b | A 23S ribosomal RNA gene tree
illustrating the phylogenetics of planctomycetes and
their relationship to a selection of other bacterial
phyla, especially those forming the Planctomycetes–
Verrucomicrobia–Chlamydiae (PVC) superphylum. The
monophyly of the PVC superphylum (arrow) was supported
regardless of the reference sequences and treeing
methods used. The arrow next to Aquificae indicates the
outgroup (the domains Archaea and Eukarya). The scale
bar represents 0.1 substitutions per nucleotide position.
Part a is modified, with permission, from REF. 29 © (2010)
US National Academy of Sciences. Part b is modified, with
permission, from REF. 38 © (2010) Society for Applied
Microbiology and Blackwell Publishing.
confined to the nuclear body, some mRNAs must be
transported through the nuclear envelope to be trans-
lated by the cytoplasmic ribosomes in the pirellulo-
some, and any nuclear proteins that are translated in
the pirellulosome must pass into the nuclear body.
The internal membrane system inside G. obscuriglobus
cells is composed of double membranes70, often with
ribo­somes aligned along these membranes; this is a
unique configuration for bacteria, in which membrane‑
associated ribosomes usually align along the cytoplas-
mic membrane. The discovery of clathrin-like membrane
coat proteins in G. obscuriglobus 71 suggests that this
organism might also possess homologues of eukaryotic
nuclear pore proteins to form structures analogous to
the nuclear pore complexes of eukaryotes. EM imaging
of serial G. obscuriglobus cell sections indicates that the
nuclear body is probably mostly enclosed by envelope
membranes. However, a recent study using electron
tomography suggests that some discontinuities, not
associated with nuclear pore complex-like structures,
may exist in the membranes that might allow direct pas-
sage of macromolecules between cell compartments70.
The membrane-bound nucleoid of G. obscuriglobus is
renewed during budding reproduction72. This occurs
via initial transfer of an apparently naked nucleoid to
the bud formed during division, followed by the forma-
tion of a new nuclear envelope in the bud via a contri­
bution from the ICM of the mother cell (to form the
inner membrane of the new nuclear envelope) and
the ICM of the newly formed bud cell (to form the outer
membrane of the new nuclear envelope).
Proteinaceous cell walls. The cell walls of plancto­mycetes
seem to be predominantly composed of proteins. This
peculiarity might reflect either the unique evolution-
ary history of these organisms or certain selective

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 REVIEWS

a wall (which is resistant to boiling in 10% sodium dodecyl

Archaea
sulphate)32,33,73. Similarly, a tyrosine–threonine–valine
(YTV) domain protein with many cysteine and pro-

icrobia
Nanoarchaeota
line residues has been identified by proteomic analysis

Halobacteria
Therm

lobi
Kor
of the cell wall of R. baltica74. Remarkably, the cell walls of

Methanom

yri
The
Th

aeog
arch

cci

ria
planctomycetes contain characteristic pits called crateri-

nop
er

rm

ococc

te
oco
Th

mo cha
es

ac
aeo
form structures, which are visible on negatively stained
opr ta
au

tha
Arch
et
pla eo

Me han
ob
m

Eu yc
ote

Me
ar

ta
cell surfaces via EM. These structures, which are distrib-

an
sm ta

i
ka om ia

t
Me
94

th
100
ct
a
i
ry 92
ot 92 94 n rob uted differently throughout the wall depending on the
Ran es
92 a
Pl imic ema
dom 92
94 100 100
lu s T repon planctomycete species, are retained in isolated cell walls.
100 E a–
reli
Bor
Gamm
aprote ydiae Similar features in related organisms. Cell compart-
obacte 100 C
hlam
ria gae
Betaproteobacte 100 T
hermoto mentalization similar to that of planctomycetes is
ria 100
also observed in various members of the PVC super-
100 92 Dictyoglomia
ria phylum, such as some verrucomicrobia 39 , lenti-
Gammaproteobacte
85
100 79 A quificae
ria 82 100
a cte 100 Nitros sphaerae (Lentisphaera araneosa)39 and poribacteria40.
proteob 92 82 82 66 pirae
Gamma c te ria 76 69
84 Mol Interestingly, members of at least one verrucomicrobial
licu
ro t eoba eria 97 Fus tes genus, Prosthecobacter, have a close homologue of the
map t
Gam bac ia 100 Ba obac
r oteo ter cil ter eukaryotic cytoskeletal protein tubulin; this protein is
a p b ac 100 89 li ia
c ria

h
Cl tino

Alp eo 94 84 more similar to tubulin than to the bacterial tubulin-

e
ona teria

rot
os

100 100
Ac noba
teo act

tri acte

ap
es

like cell division protein FtsZ75. Other verrucomicrobia

Cy roflexi
b

di

h
Chlor ia
eo

det

Chl

Alp
ba

obia

a
a
Dein
etes

Verrucom
ter

Leptospira

may encode only FtsZ, whereas some Prosthecobacter

ot

b
o
pr

obac
lta

spp. can possess both the tubulin homologue and FtsZ76.

o

Bacteroid

ococ

cte
pr

atim

r
De

ia
on

FtsZ-like proteins have also been reported to occur in

Acid

ria
sil

c
mm

icrobia
i
Ep

planctomycetes77.
Ge

Bacteria The unique anammox planctomycetes

Anammox planctomycetes are a specialized group
that forms a separate branch within the phylum. They
b Proteobacteria
carry out anaerobic oxidation of ammonium to dinitro-
Deltaproteobacteria

acteria
Maripr dans
ferroox

gen, using nitrite as an electron acceptor, with accom-

Alp

eria

panying reduction of carbon dioxide — thus, they are

Be

hap

act
proteob
ofundu

Ga
tap

p.
y

mm chemo­lithoautotrophs. However, at least some anammox

dob
rote cter

BA s
ro

I U lum

ap Elusimicrobia
plancto­mycetes may also use fatty acids such as propionate
te

Aci

ro
oba ia

p I ril
ob

te
Epsilon

as carbon sources78.
ou p
a

ob
gr ptos
cte

ac Firmicutes
te The oxidation of ammonium produces hydrazine as
ria

Le

ria
Spirochaetes
an intermediate; this is a toxic compound that is con-
verted into dinitrogen by hydrazine oxidoreductase.
Bacteroidetes
Some models for anammox metabolism have tried to
Chlorobia Fusobacteria
explain the need for the anammoxosome, a cell struc-
Dehalococcoidetes
WWE3
ture that is found only in anammox planctomycetes79
(FIG. 4a). This structure is bounded by a single bilayer
Cyanobacteria membrane, and recent evidence confirms that it is a dis-
tinctive organelle with a unique function and structure.
Chloroflexi The anammoxosome membrane contains ladderane
tes
yce P3/3
nctom O lipids (unique to anammox planctomycetes), which are
Pla Act
32
/ De ino composed of concatenated cyclobutane rings and may
OP ino
co bac possess both ester and ether links78,80–83. Ladderane lipids
ter
6

ia

1 cc
a0

3/ ia
e
crob

us confer high density to membranes and may be important

OP
era
.1.

Aqu

Th

–T
f5

he
Chlamydiae

er
ha
dc

for preventing the escape of toxic anammox interme-

comi

rm
mo
ifica
b1

tisp

us
to

diates to the pirellulosome. Both hydrazine hydrolase

e
Len

ga
Verru

PVC superphylum and hydrazine oxidoreductase are present inside the

0.10
organelle65,84. Importantly, the anammox reaction is
dependent on the separation of the anammoxosome
from the pirellulosome surrounding it, because a proton-
environmental factors (forNature Reviews | Microbiology
example, these unusual cell motive force (PMF) is generated across the anamm­
walls could have evolved as a resistance mechanism oxosome membrane by membrane ATP synthases68,85.
against lytic enzymes from predatory bacteria). In some Cytochrome c seems to be associated with the anamm­
species, a major protein has been detected that is rich oxo­some in four genera, consistent with membrane-
in proline and cysteine; the cysteine disulphide bonds in associated electron transport being needed for
this protein could be involved in stabilization of the cell generation of a PMF, as proposed in recent models

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REVIEWS

a Remarkably, the anammoxosome is packed with

Cell wall cytoskeleton-like tubules of unknown composition66.
Like other planctomycetes, anammox organisms do not
Cytoplasmic possess clear homologues of the common bacterial pro-
membrane
tein FtsZ, which forms a Z ring at the septum during
Paryphoplasm division. However, EM of ‘Ca. Kuenenia stuttgartiensis’
cells that were sectioned after cryofixation shows a dense
ring-like structure inside the paryphoplasm at the site
Nucleoid of division. Immunogold labelling demonstrated that
this structure is composed of a large, 380 kDa protein
(encoded by the locus Kustd1438) that, like FtsZ, has a
GTP-binding site90,91. The presence of a signal peptide
Pirellulosome suggests that this protein is transported across the ICM
to form the ring in the paryphoplasm, in contrast to
Intracytoplasmic FtsZ, which does not need to cross a membrane to form
membrane
0.2 µm the division ring in other bacteria. Thus, completely new
Ribosome
molecular mechanisms of cell division may be revealed
b by the planctomycetes, just as a new mechanism has
Cell wall recently been uncovered in archaea92.
Cytoplasmic
membrane ‘Endocytosis’ in Gemmata spp.
Paryphoplasm It has recently been demonstrated that the plancto­
Nucleoid mycete G. obscuriglobus has a remarkable ability for
Nuclear a bacterium: it can take up proteins from the external
envelope medium through a process that is associated with inter-
Pirellulosome nal vesicle formation and which thus resembles eukaryo-
Intracytoplasmic tic endocytosis93. Proteins are incorporated into only the
membrane paryphoplasm compartment (FIG. 5a,b) by a mechanism
500 nm
that seems to be analogous to receptor- and clathrin-
Ribosome
mediated endocytosis of eukaryotes. This is supported
Figure 3 | Cell structure of planctomycetes. Transmission electron micrographs by the presence of clathrin-like membrane coat proteins
(left) and corresponding diagrams (right) illustrating the cellNature Reviews
plan and | Microbiology
the internal in internal vesicles71 and in the membranes of isolated
membrane-defined compartments of sectioned cells of the planctomycetes Pirellula
vesicle fractions that are associated with incorporated
staleyi (part a) and Gemmata obscuriglobus (part b). In both cases, cells were prepared by
cryosubstitution before sectioning. Arrows indicate ribosomes arranged in a linear array; protein in G. obscuriglobus 93. A model analogous to
note that the aligned ribosomes are found on the inner side of the intracytoplasmic clathrin-dependent endocytosis has been proposed, in
membrane in P. staleyi (part a) and on the inner side of the nuclear membranes in which protein ligands are attached to receptors on the
G. obscuriglobus (part b). Part a micrograph is modified, with permission, from REF. 64 cytoplasmic membrane and are internalized by vesicle
© (1997) Society for General Microbiology. formation from the cytoplasmic membrane — perhaps
by formation of cages of clathrin homologues (FIG. 5c).
The membrane coat‑like proteins have been found only
for anammox biochemistry 86. The presence of ATP syn- in eukaryotes and members of the PVC superphylum,
thase within the anammoxosome membrane (as well including non-planctomycete as well as plancto­mycete
as within the ICM and the cytoplasmic membrane) of species71. These proteins belong to the coat protein
‘Ca. Kuenenia stuttgartiensis’ has been demonstrated (COP) family of proteins, members of which are essen-
using immunogold EM localization68. Moreover, 31P tial for vesicle trafficking in eukaryotic endomembrane
NMR in the same species revealed an intracellular pH systems and seem to have a role in facilitating the bend-
gradient consistent with there being two separate intra- ing of membranes. At present, it is unknown whether
cytoplasmic compartments in the cell with a pH of 7.3 planctomycetes possess homologues of other proteins
and 6.3, respectively 87. Together, these findings sup- that are known to be necessary for clathrin-mediated
port a model in which a PMF is generated across the endocytosis in eukaryotes. One might predict such
anamm­oxosome membrane (FIG. 4b). Finally, an analysis homologues, as the endomembrane system connected
of the ‘Ca. Kuenenia stuttgartiensis’ genome predicted a with endocytosis seems to have been present in the last
physico­chemically distinct subproteome for the anamm­ common ancestor of eukaryotes94,95.
oxosome88. Although there are other examples of inter- Uptake of proteins from the external milieu by
Anammoxosome
An organelle within the nal organelles that generate a PMF in bacteria, such as endocytosis is a mode of nutrition that is found only in
pirellulosome of anammox the thylakoids of cyanobacteria89 (in which the direction eukaryotes and planctomycetes. Little is known about
planctomycetes that is and magnitude of the PMF are similar to those of the its importance for the ecology and evolution of plancto­
surrounded by a single bilayer anammoxosome PMF but the energy source is differ- mycetes, but it could be key to explaining how and why
membrane and contains
enzymes that are essential
ent), the anammoxosome can in some ways be seen as a these organisms evolved their internal membranes and
for the oxidation of ammonia bacterial analogue of the eukaryotic mitochondrion, as correlated features. It might even provide a model for
to dinitrogen. both organelles generate non-photosynthetic PMFs. adaptations that originally selected for a nucleus and

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© 2011 Macmillan Publishers Limited. All rights reserved

 REVIEWS

a The function could be predicted for only 32% of

Anammoxosome the ORFs in the 7.1 Mb circular genome of R. baltica;
membrane
although the proportions of ORFs with a predicted func-
Intracytoplasmic
membrane tion were somewhat higher in P. staleyi and P. limno­
Cytoplasmic philus (around 54%), hypothetical proteins are a feature
membrane of planctomycetes, and this remains a challenge for
Anammoxosome
Anammoxosome understanding the molecular cell biology of these
Cell wall
bacteria.
R. baltica lacks genes encoding key crosslinking
enzymes that are used in the late stages of peptido­glycan
Pirellulosome
synthesis. It possesses genes that putatively encode
Nucleoid
enzymes for standard chemoheterotrophic pathways
250 nm Paryphoplasm
Ribosome (for example, heterolactic fermentation), as well as 110
genes that encode products with homology to the sul-
b phatases of bacteria and eukaryotes and that might have
NO2 NH4+ a role in the degradation of sulphated glyco­polymers
such as those in marine-snow aggregates. These sul-
N2H4
phatases could be useful as industrial catalysts 99,100.
Nir NO Hh Hao N2
Transcriptomic studies indicated that these sulphatases
1e
– 3e– 4e
– may also be involved in the formation of disulphide
c c c bridges in cell wall proteins101.
6H+ Consistent with the unusual planctomycete cell wall,
+ Anammoxosome R. baltica lacks genes encoding the components of the
bc1
bacterial FtsZ-dependent divisome, with the only excep-
Q
tion being the presence of the gene encoding FtsK.
– Pirellulosome 3H+ ATPase R. baltica has numerous genes encoding RNA polymer-
ase σ-factors that may have a role in gene regulation dur-
ADP + P ATP ing the bacterial life cycle or cell differentiation102. Some
gene products of R. baltica contain a novel signal pep-
Figure 4 | Anammox planctomycetes. a | A transmission electron micrograph of a
Nature
section of cryosubstituted ‘Candidatus Kuenenia stuttgartiensis’ Reviews
(left), Microbiology
and a| schematic
tide motif that has not been detected in other plancto­
of the cell plan of anammox planctomycetes (right). The micrograph shows the internal mycetes and that might target proteins for export to the
compartmentalization of a cell that has been labelled with immunogold to locate the cell surface. This signal peptide occurs in proteins that
catalytic β-subunit of F‑ATPase. Gold particles on the anammoxosome membrane are contain calx‑β domains or domains with similarity to
indicated by arrows. b |  A model for anammox biochemistry, which is dependent on the thrombo­spondin type 3 repeats or cadherin domains, all
unique type of compartmentalization in these planctomycetes. The catabolic anammox of which are involved in cell–cell interactions in eukary-
reactions coupled over the anammoxosome membrane result in electron transport via otes. Moreover, some proteins containing a plancto­
cytochrome c and consequent translocation of protons from the pirellulosome to the mycete-specific cytochrome 1 domain also contain a
anammoxosome. The resulting proton gradient generates a proton-motive force that discoidin domain, which is associated with cell adhesion
drives subsequent ATP synthesis via the membrane-embedded ATPase. bc1, cytochrome bc1
in eukaryotes. Although many novel planctomycete-
complex; Hao, hydrazine–hydroxylamine oxidoreductase; Hh, hydrazine hydrolase;
Nir, nitrite reductase; Q, coenzyme Q. Parts a and b are modified, with permission, from
specific protein domains are predicted to be extra­cellular,
REF. 68 © (2010) Blackwell Publishing.
it seems just as likely that the corresponding proteins are
transported across internal membranes such as the ICM,
perhaps to accumulate in the paryphoplasm, rather than
endomembrane system (for example, the model sug- secreted to the external milieu.
Heterolactic fermentation
gested by De Duve for the evolution of endomembranes Detailed proteomic studies have been carried out
A pathway for anaerobic
fermentation of carbohydrates; in eukaryotes96). with R. baltica str. SH 1 (REFS 74,103–105), and proteins
typically found in lactic acid have been shown to be distributed differentially among
bacteria, in which the dominant Insights from genomics and proteomics cell compartments of this organism103. For instance,
end products are lactic acid, At present, only one complete genome of a plancto­mycete housekeeping proteins such as glycolysis enzymes lack
ethanol and carbon dioxide.
has been described in detail in the literature — that signal peptides and may be confined to the pirellulo-
Divisome of R. baltica (originally classified as Pirellula sp. str. 1)35 some, whereas other proteins, such as some sulphatases,
A complex of proteins that is — with features of two other genomes, from Pirellula do carry signal peptides and may be translocated into
associated with cell division in staleyi and Planctomyces limnophilus, described in the paryphoplasm.
peptidoglycan-synthesizing
summary form only 97,98. Data for complete genomes of The draft 4.2 Mb genome of the anammox plancto-
bacteria and that locates to
the septum of cells dividing by Blastopirellula marina, Planctomyces maris, Planctomyces mycete ‘Ca. Kuenenia stuttgartiensis’ was assembled in
binary fission. The complex brasiliensis and Isosphaera pallida are also available a metagenomic analysis of the mixed microbial com-
includes cell division protein (see Databases). Other species, such as G. obscuri­ munity from a bioreactor 28. Genes putatively encod-
FtsZ and, usually, other globus, have only draft genomes available. The genome ing a complete acetyl-CoA pathway for carbon dioxide
proteins such as FtsI, FtsA and
FtsK, as well as penicillin-binding
of P. limnophilus includes a 37 kb plasmid as well as a fixation and a cytochrome cd1 nitrite–nitric oxide oxido­
proteins involved in 5.5 Mb chromosome, but the 6.2 Mb genome of P. staleyi reductase (NirS) were detected, allowing a revision of
peptidoglycan synthesis. consists of a single circular chromosome. the model for anammox metabolism to include nitric

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REVIEWS
a b Paryphoplasm
Nucleoid
10 μm 500 nm
Nuclear envelope
c
Cell wall Cytoplasmic membrane
GFP
Membrane coat-like protein
Protein receptor
Figure 5 | An endocytosis-like process in planctomycetes. a | A fluorescence
Nature Reviews | Microbiology
micrograph illustrating endocytosis-like uptake of GFP by Gemmata obscuriglobus. GFP is
green, the cytoplasmic membrane is red (stained with SynaptoRed), and the DNA of the
nucleoid is blue (stained with 4′,6‑diamidino‑2‑phenylindole (DAPI)). Note that GFP is
localized to a distinct compartment that is separate from the DNA. b | A transmission
electron micrograph of a sectioned cryosubstituted G. obscuriglobus cell, illustrating
internal GFP that has been incorporated by an endocytosis-like process. The 10 nm
colloidal gold particles (arrows) result from immunogold labelling using a GFP-specific
antibody and are localized only in ribosome-free, electron-dense paryphoplasm regions.
c | A model for the receptor-mediated endocytosis-like mechanism in G. obscuriglobus.
The diagram shows the suggested stages for the GFP uptake process described in
parts a,b. The model is based on electron micrographs and immunolabelling of sectioned
cells, as well as on the analysis of subcellular fractions isolated from lysed cells. Stage 1
involves the binding of GFP ligand in the external milieu to receptors in the cytoplasmic
membrane. Stages 2 and 3 are the initial steps of plasma membrane invagination and the
association of GFP with vesicles that are in the process of being generated, respectively.
At the final stage, vesicle formation is complete. In this model, membrane coat‑like
(clathrin-like) proteins coat the outside of the vesicle via cage formation, and the GFP
ligands become oriented to the inside membrane surface of the vesicle during its
formation, owing to the effect of infolding. Infolding and formation of vesicles occurs in
the paryphoplasm. Part b is reproduced and part c is modified, with permission, from
REF. 114 © (2010) Landes Bioscience.
oxide as an intermediate. The genomic analysis sug-
gested that diverse electron acceptors can be used, and it
was confirmed experimentally that both iron oxide and
manganese oxide were used as electron acceptors
and that iron could also act as an electron donor. Thus,
iron oxidation as well as iron, manganese and nitrate
reduction were added to the physiological range of this
presumed specialist. These results suggest a wider bio­
geochemical role than previously predicted for anammox
bacteria, in addition to their known importance for the
global nitrogen cycle. Interestingly, transfer of nitri-
fication genes such as that coding for nitrite oxido­
reductase (NXR) between anammox planctomycetes and
410 | JUNE 2011 | VOLUME 9 www.nature.com/reviews/micro
© 2011 Macmillan Publishers Limited. All rights reserved
nitrite-oxidizing bacteria of the phylum Nitrospirae can
occur in activated sludge106.
A comparative analysis of the available plancto­mycete
genomes with that of ‘Ca. Kuenenia stuttgartiensis’ (REF. 5)
has suggested that the anammox and non-anammox
planctomycetes are distinct from each other, as many
genes shared by heterotrophic planctomycetes are
absent or sparse in ‘Ca. Kuenenia stuttgartiensis’. This
was especially clear for the subset of genes for tetra­
hydromethanopterin (H4MPT)-dependent C1 carbon
metabolism, which are present in R. baltica, G. obscuri­
globus, P.  maris, B.  marina and even some marine
planctomycete sequences, but absent in ‘Ca. Kuenenia
stuttgartiensis’.
Complete but formally undescribed genomes for other
planctomycetes are available, such as those of P. maris and
B. marina, and a draft genome for G. obscuriglobus is also
available for analysis, so the foundations are starting to
be laid for comparative genomics to assist in the interpre-
tation of planctomycete cell biology. Interestingly, some
homologues of typically eukaryotic proteins have been
found in G. obscuriglobus 107 and Gemmata sp. Wa1‑1
(REF. 108) (a soil strain for which some draft genomic
data are publicly available).
The absence of genetic systems for planctomycetes is
a serious barrier to progress concerning the molecular
and cell biology of these bacteria, but some laborato-
ries are now attempting to develop these systems. Such
systems are central to future experimental progress
using techniques such as GFP fusions and transposon
mutagenesis to study functional aspects of the internal
compartments, the membranes and transport between
compartments, as well as the cell cycle and physiology
of these organisms.
Implications for the origin of eukaryotes
The presence of eukaryote-like characteristics, such as
nucleoid compartmentalization and endocytosis-like
protein uptake, in planctomycetes can be explained by
at least four different models. According to one model,
planctomycetes retained some eukaryotic cell charac-
teristics, and the relevant genes, from a eukaryote-like
common ancestor — perhaps even from a eukaryote-
like last universal common ancestor (LUCA), ances-
tral to the three domains of life. Thus, planctomycetes
may have descended reductively from a more complex
eukaryote-like cell that possessed membrane coat‑like
proteins for endocytosis-like nutrition109. A second
scenario assumes that planctomycetes evolved various
eukaryote-like features (for example, compartmentaliza-
tion, the endomembrane system and endocytosis), and
the genes coding for these features were later transferred
to a very early proto-eukaryote of the eukaryotic nuclear
lineage, which became a common ancestor to all modern
eukaryotes. A third model suggests that plancto­mycetes
evolved eukaryote-like characteristics via parallel con-
vergent evolution alongside the eukaryote ancestor,
owing to similar adaptive needs and selective pressures,
and that there is no homology between those character-
istics in planctomycetes and eukaryotes, only analogy
in structure (for example, a similarity in the secondary
 REVIEWS

protein structure does not reflect homology in the pri-
mary structure). In a fourth scenario, lateral gene trans-
fer from evolved eukaryotes occurred, but this must
have been both ancient and extensive. New data on the
molecular nature of eukaryote-like features of plancto­
mycetes are needed to allow us to choose between the
different models.
Nevertheless, it seems clear that the planctomycetes
are now a strong challenge to the idea that some form of
fusion between archaeal and bacterial cells was necessary
to evolve the eukaryote and its nucleus. If autogenous
development of internal membranes can result in envel-
opment of the nucleoid by a membrane or membranes
and can also result in an endomembrane system that is
able to provide an endocytosis-like mechanism, then
symbiotic fusions between cell types are not necessary
to bring about these features. Such fusions are already
less plausible than was first thought for other reasons,
such as the absence of any contemporary example of
engulfment between bacterial and archaeal cells110. The
challenge remains to determine whether plancto­mycetes
represent a precursor of eukaryotes, the retention of
certain characteristics of a proto-eukaryotic LUCA, or a
convergent re-evolution of a eukaryote-like plan.
Conclusions and future directions
Planctomycetes display rare properties that, in many
cases, can be related to their compartmentalized cell
plan. Thus, studying the molecular details of the com-
partmentalized cell plans of both planctomycetes and
their PVC relatives may be key to understanding the
nutrition, physiology, ecology and evolution of these
extraordinary organisms. This has already proved to
be the case for anammox planctomycetes. Such insights
can be seen in the context of the increasing apprecia-
tion of bacterial cell structure and biology, and of the
increasingly blurred boundaries between ‘prokaryotic’
and ‘eukaryotic’ molecular cell biology — for example,
the discovery of lipid rafts in Bacillus spp.111, the bud-
ding of vesicles from the membranes of photosynthetic
bacteria112, and paracrine as well as autocrine signal-
ling in bacterial biofilms113. The discovery of endo-
cytosis-like protein uptake in G. obscuriglobus was an
important finding, and the implications of this discov-
ery for our understanding of the evolution of eukaryo-
tic endomembranes and eukaryotic cell biology need
to be further explored. One particular area of interest
concerns whether planctomycetes have homologues of
the many genes involved in membrane trafficking and
in the formation of endomembranes in eukaryotes, or
whether instead many of the functions of these eukary-
otic genes are performed by functional analogues in
planctomycetes.
There is also a pressing need to develop genetic
systems for model planctomycetes and to cultivate
anammox planctomycetes in pure culture. The life cycle
of some planctomycetes involves swarmer and sessile cells
analogous to those of the established Caulobacter crescentus
model, and this similarity invites opportunities for com-
parative developmental genetics104. Nevertheless, we
have already learned much about planctomycete biology
using tools such as proteomics, transcriptomics and fluo-
rescence microscopy, as well as bioinformatics applied to
structural biology (which is needed to reveal significant
homology to eukaryotic proteins). The meaning and
implications of the fact that several features, such as cell
compartmentalization and sterol synthesis, are shared by
members of the PVC superphylum need to be explored.
It would also be very interesting to know whether
plancto­mycetes can form useful models for the study of
some aspects of chlamydial biology, especially if a genetic
system for planctomycetes can be constructed.
In studying the cell biology of planctomycetes,
we may well be studying the first traces of the evolu-
tion of our own cell biology. We may even share with
these organisms more than just a house with the same
floor plan: shared molecular bricks and mortar corre-
lated with such a compartmentalized plan might also
be found. The planctomycetes could be at the heart of
understanding how the first eukaryote-like cell, organ-
ized with a plan that is essentially that of our own cells,
came about. We foresee that future research on plancto-
mycetes will be highly productive, not only because of
their environmental and biotechnological significance,
but also because planctomycetes might supply the
necessary tools for digging deep into our own past.

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Acknowledgements
Research on planctomycetes in the J.A.F. laboratory is sup-
ported by the Australian Research Council (ARC Discovery
Project DP0881485).
Competing interests statement
The authors declare no competing financial interests.
DATABASES
Entrez Genome Project for planctomycetes:
http://www.ncbi.nlm.nih.gov/genomeprj?term=
planctomycetes
Blastopirellula marina | Gemmata obscuriglobus | Isosphaera
pallida | Pirellula staleyi | Planctomyces brasiliensis |
Planctomyces limnophilus | Planctomyces maris |
Rhodopirellula baltica
FURTHER INFORMATION
John A. Fuerst’s homepage:
http://www.scmb.uq.edu.au/staff/john-fuerst
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