Article

Widespread Distribution of Poribacteria in Demospongiae

Abstract and Figures

Poribacteria were found in nine sponge species belonging to six orders of Porifera from three oceans. Phylogenetic analysis revealed four distinct poribacterial clades, which contained organisms obtained from several different geographic regions, indicating that the distribution of poribacteria is cosmopolitan. Members of divergent poribacterial clades were also found in the same sponge species in three different sponge genera.
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APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Sept. 2009, p. 5695–5699 Vol. 75, No. 17
0099-2240/09/$08.000 doi:10.1128/AEM.00035-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
Widespread Distribution of Poribacteria in Demospongiae
Feras F. Lafi,
1
John A. Fuerst,
1
* Lars Fieseler,
2
† Cecilia Engels,
2
Winnie Wei Ling Goh,
1
and Ute Hentschel
2
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia,
1
and
Research Center for Infectious Diseases, University of Wu¨rzburg, Ro¨ntgenring 11, D-97070 Wu¨rzburg, Germany
2
Received 7 January 2009/Accepted 21 June 2009
Poribacteria were found in nine sponge species belonging to six orders of Porifera from three oceans.
Phylogenetic analysis revealed four distinct poribacterial clades, which contained organisms obtained from
several different geographic regions, indicating that the distribution of poribacteria is cosmopolitan. Members
of divergent poribacterial clades were also found in the same sponge species in three different sponge genera.
Recently, a novel bacterial phylum, termed “Poribacteria,”
was discovered, and members of this phylum have been found
exclusively in sponges (2). Phylogenetic analyses of 16S rRNA
genes indicated that poribacteria are evolutionarily deeply
branching organisms and related to a superphylum composed
of Planctomycetes,Verrucomicrobia, and Chlamydia (11). Pori-
bacterial 16S rRNA genes contain 13 of 15 planctomycete
signature nucleotides, but a level of sequence divergence of
more than 25% compared to any other bacterial phylum, in-
cluding the Planctomycetes, justifies the status of this taxon as
an independent phylum. A consistent treeing pattern is difficult
to resolve in comparative phylogenetic sequence analyses,
making the poribacteria an unusual line of phylogenetic de-
scent. In addition to their divergent status as a separate phylum
on the basis of the 16S rRNA sequence, poribacteria are also
divergent because they may have a compartmentalized cell
structure, a cell plan they share only with members of the phyla
Planctomycetes and Verrucomicrobia (2). They are also of in-
terest for understanding the potential contribution of obligate
sponge-associated bacteria to the sponges harboring them and
as an example of a yet-to-be-cultured group of bacteria asso-
ciated with invertebrate tissue apparently exclusively but for
unknown reasons. This study aimed to further explore the
presence and diversity of poribacteria in different marine
demosponge genera using samples from around the world.
The Mediterranean sponges were collected by scuba divers
offshore at Banyuls sur Mer, France (42°29N, 03°08E). The
Caribbean sponges were collected offshore at Little San Sal-
vador Island, Bahamas (24°32N, 75°55W). The eastern Pa-
cific sponge Aplysina fistularis was collected offshore at San
Diego, CA (32°51N, 117°15W). The western Pacific sponge
Theonella swinhoei was collected offshore at Palau (07°23N,
134°38E). All non-Great Barrier Reef (non-GBR) sponges
were collected between May and July 2000, and once individ-
ual sponge specimens were brought to the surface, they were
frozen in liquid nitrogen on board ship and stored at 80°C
until microbiological processing (9). The GBR marine sponges
were collected off Heron Island Research Station (23°27S,
151°5E) in April 2002 (5). Pseudoceratina clavata was col-
lected by scuba divers at a depth of 14 m, and Rhabdastrella
globostellata was collected at a depth of ca. 0.5 m after a reef
walk consisting of a few hundred meters. The samples were
immediately placed in plastic bags and brought to Heron Is-
land Research Station, where they were stored at 80°C until
processing. Sponge DNA was extracted as described previously
(2, 5).
Total sponge-derived genomic DNA was screened by PCR
for the presence of poribacteria using a 16S rRNA gene primer
set. Poribacterial 16S rRNA genes were amplified by employ-
ing a pair of Poribacteria-specific primers, POR389f (5-ACG
ATG CGA CGC CGC GTG-3) and POR1130r (5-GGC
TCG TCA CCA GCG GTC-3) (2). The poribacterial PCR
products that were ca. 740 bp long derived from one sponge
individual were cloned into the pGEM-T Easy vector (Pro-
mega, Madison, WI). Clone inserts were digested with restric-
tion endonucleases MspI and HaeIII (New England Biolabs,
Inc., United States), characterized to obtain restriction profiles
and unique profiles, and sequenced. The compiled partial 16S
rRNA gene sequences were then analyzed using BLASTN to
select the most closely related poribacterial reference se-
quences.
The sequences exhibiting levels of similarity of less than 97%
were used for further analysis. Poribacterial 16S rRNA gene
sequences were aligned using the ARB software package (7).
The resulting alignment was imported into PAUP (10) and
analyzed by using distance, maximum parsimony, and maxi-
mum likelihood algorithms together with bootstrap resam-
plings (3,000, 3,000, and 200 resamplings, respectively), and the
resulting bootstrap values were applied to nodes on the ARB
neighbor-joining tree. Signature sequences were detected us-
ing the ARB software package. A signature sequence is de-
fined here as a short sequence that is present in a group of
poribacterial sequences in a phylogenetic clade but is not
found in any other clade in the poribacterial tree.
Analysis of the 16S rRNA gene clone library sequences
generated from sponge tissues revealed the presence of pori-
bacteria in sponge individuals belonging to the orders Verongida,
Astrophorida, Dictyoceratida, Haplosclerida, Lithistida, and
Homosclerophorida, while poribacteria could not be detected
* Corresponding author. Mailing address: School of Chemistry and
Molecular Biosciences, The University of Queensland, Brisbane,
Queensland 4072, Australia. Phone: (49) 931 312581. Fax: (49) 931
312578. E-mail: j.fuerst@mailbox.uq.edu.au.
Present address: Institute for Food Science and Nutrition, ETH
Zurich, Schmelzbergstrasse 7, CH-8092 Zurich, Switzerland.
Published ahead of print on 26 June 2009.
5695
in sponges belonging to the orders Hadromerida and Agela-
sida. In the order Halichondrida, poribacteria were detected in
Xestospongia muta but not in Haliclona sp. Altogether, nine
sponge species were added to the list of Poribacteria-containing
sponges (Table 1). Three distinct clades were observed that
were clearly supported by bootstrap values greater than 75 with
every tree-building algorithm applied (Fig. 1), and one clade
(clade I) was supported by bootstrap values of 64, 98, and 71 in
distance, maximum parsimony, and maximum likelihood trees,
respectively. Similarity calculations using approximately
740-bp amplified poribacterial 16S rRNA gene fragments and
other poribacterial sequences from the NCBI database showed
TABLE 1. Distribution of poribacteria in different demosponge orders
Sponge species or seawater Order Geographic location
a
Presence of
poribacteria
b
Reference
Aplysina aerophoba Verongida MED 2
Aplysina lacunosa Verongida BAH 2
Aplysina fistularis Verongida EPAC or BAH 2
Aplysina insularis Verongida BAH 2
Verongula gigantea Verongida BAH 2
Smenospongia aurea Dictyoceratida BAH 2
Aplysina cauliformis Verongida BAH This study
Aplysina archeri Verongida BAH This study
Aplysina cavernicola Verongida MED This study
Pseudoceratina clavata Verongida WPAC This study
Rhabdastrella globostellata Astrophorida WPAC This study
Ircinia sp. Dictyoceratida BAH This study
Xestospongia muta Haplosclerida BAH This study
Theonella swinhoei Lithistida EPAC This study
Plakortis sp. Homosclerophorida BAH This study
Chondrilla nucula Hadromerida BAH 2
Agelas wiedenmayeri Agelasida BAH 2
Agelas cerebrum Agelasida BAH This study
Axinella polypoides Halichondrida MED This study
Ptilocaulis sp. Halichondrida BAH 2
Dysidea avara Dictyoceratida MED This study
Haliclona sp. Haplosclerida MED This study
Ectyoplasia ferox Poecilosclerida BAH 2
Seawater NA
c
MED This study
a
MED, Mediterranean Sea; BAH, Bahamas; WPAC, western Pacific Ocean; EPAC, eastern Pacific Ocean.
b
The presence of poribacteria was evaluated by sequencing and phylogenetic analysis of amplified PCR products. , present; , absent.
c
NA, not applicable.
FIG. 1. Neighbor-joining phylogenetic tree for poribacterial clones based on Poribacteria-specific PCR products (740 bp) of the 16S rRNA gene,
showing relationships of poribacterial clones from different global regions. The poribacterial clones on the right are additional clones belonging
to the same clades as strains in the tree at the same level. Bootstrap confidence values of 75% for distance, maximum parsimony, and maximum
likelihood algorithm analyses are indicated by filled circles at nodes, and open circles indicate unsupported nodes. Prefixes for clones: A, Aplysina
aerophoba;C,Aplysina cavernicola;F,Aplysina fistularis;L,Aplysina lacunosa;S,Ircinia sp.; P, Plakortis sp.; PC, Pseudoceratina clavata; RG,
Rhabdastrella globostellata;T,Theonella swinhoei;X,Xestospongia muta. Scale bar 0.1 nucleotide substitution per site.
5696 LAFI ET AL. APPL.ENVIRON.MICROBIOL.
that the dissimilarity between clades was consistent with their
separation in phylogenetic trees. For example, the levels of
dissimilarity between members of clade I and clade II were 3 to
8%, while the levels of dissimilarity between members of clades
I and III and between members of clades I and IV were 10 to
14% and 11 to 15%, respectively.
Within each clade in the phylum Poribacteria, there were
higher similarity values, including 94 to 100% among members
of clade I, 94 to 99% among members of clade II, 96 to 99%
among members of clade III, and 96 to 99% among members
of clade IV. When members of the the phylum Poribacteria
were compared to members of the Planctomycetes (Fig. 1), the
16S rRNA genes exhibited levels of sequence dissimilarity of
up to 38%, consistent with the conclusion of Fieseler et al.
concerning the separate phylum level status of poribacteria
based on a similarity value of 75%. A phylogenetic correla-
tion between sponge phylogeny and poribacterial phylogeny is
not evident, since, for example, clones from A.fistularis and
Aplysina aerophoba occurred in both clade I and clade II and
one clone from A. aerophoba also occurred in clade III, while
clones from P.clavata and R.globostellata occurred in clades I,
II, and III but not in clade IV. Clades I and II included
poribacterial clones derived from all sponge species occurring
in all of the widely separated geographic regions examined in
this study (Fig. 2). Clade III represented poribacterial clones
derived from sponge species obtained in the eastern Pacific
region, GBR, and the Bahamas but not in the Mediterranean
region. The majority of poribacterial clones in clade IV were
derived from sponge species obtained in the Bahamas, and one
clade IV clone was obtained from a sponge species collected in
the Mediterranean region.
Poribacterial clones from different sponges from widely sep-
arated marine habitats belonged to at least four major clades
with similarities ranging from 94 and 96%. For clade III (Fig.
1), we detected a signature sequence characteristic of poribac-
terial clones from the GBR sponges R.globostellata and P.
clavata. This signature sequence (CCA GTT AGC TTG ACG
GTA) (Table 2) at E. coli positions 469 to 487 targeted 10
sequences, 5 of which were from GBR marine sponges gener-
ated in this study (clones RG68, RG112, RG105, PC96, and
PC8). Another five poribacterial sequences were detected in an
unpublished study investigating the microbial diversity in GBR
sponges. This signature sequence indicates a specific geo-
graphic presence of poribacteria belonging to clade IV in the
GBR region. In addition, a sequence (GAG TGT GAA ATG
GCT TGG at E. coli positions 599 to 617) characteristic of
clade IV was found in 11 sequences derived from sponges from
the Bahamas and one sequence (A7) from a Mediterranean
sponge.
Based on the data presented here, Poribacteria appears to be
a bacterial phylum that is specifically found in several demo-
sponge genera of the phylum Porifera (Table 1). To our knowl-
edge, this is the only case of a bacterial phylum specifically
associated with a marine invertebrate phylum. Certain phylum
members appear to be widely distributed among sponges be-
longing to different species and in different geographic regions,
forming sponge-specific lineages (3), but these are individual
species level or at most genus level clades in a subdivision of a
phylum rather than in a whole phylum.
PCR analyses of seawater samples collected in this study
(Table 1) and searches using nucleotide sequence databases of
seawater metagenomes were negative for poribacteria. This is
consistent with the concept that Poribacteria is a sponge-spe-
cific phylum. Within the sponges poribacteria are distributed
FIG. 2. Neighbor-joining phylogenetic tree for poribacterial clones based on Poribacteria-specific PCR products (740 bp) of the 16S rRNA gene,
showing the internal relationships of and occurrence of clade I members in distinct sponge species representing cosmopolitan geographic regions.
For an explanation of the colors, see Fig. 1. Bootstrap confidence values of 75% for distance, maximum parsimony, and maximum likelihood
algorithm analyses are indicated by filled circles at nodes, and open circles indicate unsupported nodes. Prefixes for clones: A, Aplysina aerophoba;
C, Aplysina cavernicola;F,Aplysina fistularis;L,Aplysina lacunosa;S,Ircinia sp.; P, Plakortis sp.; PC, Pseudoceratina clavata; RG, Rhabdastrella
globostellata;T,Theonella swinhoei;X,Xestospongia muta. Scale bar 0.1 nucleotide substitution per site. Clones PC15, L8, T6, C2, P3, S2, and
X1 were removed from this analysis to allow better branch resolution.
VOL. 75, 2009 DISTRIBUTION OF PORIBACTERIA 5697
among members of distinct demosponge orders that occur in
various geographic locations, indicating that there is wide dis-
tribution of poribacteria among marine demosponges. Very
similar 16S rRNA clone sequences that cluster in clade I were
found in sponges from all geographic regions sampled in this
study, including locations in the Northern and Southern hemi-
spheres (Fig. 2). Similarly, clade II contains poribacterial
clones from the Mediterranean Aplysina species and from
GBR Pseudoceratina and Rhabdastrella species. This appears
to contrast, albeit at a lower level of resolution, with results
suggesting that bacterial populations are endemic in different
geographic regions, e.g., with the findings that marine bacte-
rioplankton communities include few cosmopolitan opera-
tional taxonomic units (8), that fluorescent Pseudomonas ge-
notypes from soil are endemic at different geographic sites (1),
and that hyperthermophilic Sulfolobus archaea from different
geothermal areas are genetically divergent (12). Judging the
endemicity of populations in different geographic regions may
depend on the taxonomic scale used to distinguish populations
(1). In this study we provide evidence that at least some clades
may be relatively characteristic of particular regions, e.g., GBR
clade III (Table 2). It is remarkable that in the case of the
sponge species R.globostellata and P.clavata from a single
geographic region (GBR), the microbial communities include
representatives of distantly related poribacterial clades II and
III, whose sequences exhibit levels of dissimilarity ranging
from 10 to 13%. In another case poribacteria belonging to
clades I, II, and IV were found in a single host, A.aerophoba,
from the Mediterranean. Thus, members of widely divergent
poribacterial clades occur in the same specimen in sponges in
widely separated geographic regions in the world’s oceans.
Three different sponge species belonging to three different
genera exhibit this phenomenon.
The morphology and life strategy of sponges have remained
unchanged for the past 580 million years, as judged by the
dramatic similarity of the morphologies of Precambrian fossils
to the morphologies of recent sponges (6). Adaptation of the
poribacteria to this niche might have taken place early in evo-
lution before the various sponge orders separated from each
other. It seems likely that poribacteria diverged from other
bacterial phyla long before evolution of the metazoans as part
of the fan-like radiation by which all bacterial phyla appear to
have arisen (4). This bacterial radiation may have resulted in
the divergence of the clades that we have observed for the
poribacteria, but there is no indication of cospeciation between
host sponges and the poribacteria.
In summary, poribacteria exhibit considerable diversity and
are classified into four phylogenetic clades. Poribacteria seem
to be widely distributed among many different marine demo-
sponge genera, and further studies are needed to explain the
nature of the poribacterium-sponge interaction.
Nucleotide sequence accession numbers. 16S rRNA gene
sequences obtained in this study have been deposited in the
EMBL/GenBank/DDBJ databases under accession numbers
EU071627 to EU071680.
We thank the marine operations personnel at the Institute Rudjer
Boscovic (Rovinj, Croatia) for excellent support, as well as the captain
and crew of the R/V Seaward Johnson (HBOI, Florida) for their help
during sponge collection. We thank Mary Garson and John Hooper for
assistance with collection and identification of GBR sponges from
Australia.
Financial support was provided by a Deustche Forschungsgemein-
schaft SFB567 grant (TP C3) to U.H. and by grants from the Austra-
lian Research Council and the University of Queensland to J.A.F.
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TABLE 2. Poribacterial signature sequences for clades III and IV, including a GBR-specific signature sequence (pori_SSIII) and a signature
sequence specific to 11 of 12 sequences from the Bahamas (pori_SSIV)
Signature
sequence Name Full name
a
E. coli
position Sequence
b
pori_SSIII Pla101P Pla101P* 469 GGUGAUAAG-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CCAUAGUA
Pla131P Pla131P* 469 GGUGAUAAG-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CCAUAGUA
Pla134P Pla134P* 469 GGUGAUAAG-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CCAUAGUA
Pla50P Pla50P* 469 GGUGAUAAG-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CCAUAGUA
Pla82P Pla82P* 469 GGUGAUAAG-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CCAUAGUA
PO68 Pori clone RGPo68 469 GGUGAUAAG-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-GAGAAAAG
PO112 Pori clone RGPo112 469 GGUGAUAAU-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CCAUAGUA
PO105 Pori clone RGPo105 469 GGUGAUAAG-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CCAUAGUA
PO96 Uncultured Pori clone 469 GGUGAUAAG-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CCAUAGUA
PCPO8 Pori clone PCPo8 469 GGUGAUAAG-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CCAUAGUA
pori_SSIV AY485286 Uncultured Pori clone 599 ACAUUAGUC-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CUCAACCA
AY485285 Uncultured Pori clone 599 ACAUNAGUC-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CUCAACNA
AY485284 Uncultured Pori clone 599 ACAUUAGUC-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CUCAACCA
AY485281 Uncultured Pori bacterium 599 ACAUUAGUC-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CUCAACCA
A7 A7 599 AUAUUAGUC-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CUCAACCA
F2 F2 599 ACAUAAGUC-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CUCAACCA
L16 L16 599 ACAUUAGUC-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CUCAACCA
P20 P20 599 ACAUAAGUC-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CUCAACCA
P38 P38 599 ACAUUAGUC-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CUCAACCA
S6 S6 599 AUAUUAGUC-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CUCAACCA
S10 S10 599 AUAUUAGUC-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CUCAACCA
X18 X18 599 ACAUUAGUC-⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽⫽-CUCAACCA
a
Asterisks indicate poribacterial clones derived from the GBR sponge R. globostellata in a separate study.
b
The internal sequence (indicated by equals signs) of each pori_SSIII clone is CCAGUUAGCUUGACGGUA, and that of each pori_SSIV clone is GAGUGU
GAAAUGGCUUGG.
5698 LAFI ET AL. APPL.ENVIRON.MICROBIOL.
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Supplementary resources (54)

... Other factors, such as collection site or depth, could not explain the observed trend. Similar incongruence of symbiont and host phylogeny was observed for the Entoporibacteria (34 homologous genes used to estimate synonymous substitution rates) ( Fig. 4C and D), in agreement with previous phylogenetic studies (34,36,37). This would suggest that these sponges likely acquired a free-living Tethybacterales common ancestor at different time points throughout their evolution and that the same is true for the Entoporibacteria. ...
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The fossil record indicates that the earliest evidence of extant marine sponges (phylum Porifera) existed during the Cambrian explosion and that their symbiosis with microbes may have begun in their extinct ancestors during the Precambrian period. Many symbionts have adapted to their sponge host, where they perform specific, specialized functions. There are also widely distributed bacterial taxa such as Poribacteria, SAUL, and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added 11 new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these symbionts appear to preferentially associate with low-microbial abundance (LMA) and high-microbial abundance (HMA) sponges, respectively. Within these sponges, we show that these symbionts likely perform distinct functions and may have undergone multiple association events, rather than a single association event followed by coevolution. IMPORTANCE Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three known bacterial taxa (Entoporibacteria, SAUL, and Tethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. Finally, it appears that the Entoporibacteria are associated primarily with high-microbial abundance sponges, while the Tethybacterales associate with low-microbial abundance sponges.
... In fact, sponge-associated microorganisms are of great interest because of their potential role in producing several compounds (Montalvo and Hill 2011;Moitinho-Silva et al. 2017). Several studies of marine sponges-related bacteria have identified novel bacterial groups, such as the candidate phylum Poribacteria (Lafi et al. 2009). Moreover, bacteria also play a significant role in eliminating polycyclic aromatic hydrocarbons (PAHs) from contaminated habitats but, the potential use of marine sponges with symbiont bacteria is still unexplored (Marzuki 2018). ...
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Marzuki I, Kamaruddin M, Ahmad R. 2021. Identification of marine sponges-symbiotic bacteria and their application in degrading polycyclic aromatic hydrocarbons. Biodiversitas 22: 1481-1488. Diverse and abundant microbial species that occupy marine sponges may make important contributions to host metabolism. Sponges are filter feeders and devour microorganisms from the seawater around them. Each microbe that endures the sponges’ digestive and immune responses are related symbiotically. Marine sponges symbiont bacteria can comprise as much as 40% of sponge tissue volume, and these are known to exhibit a great potential on polycyclic aromatic hydrocarbons (PAHs) degradation. However, the potential use of marine sponges symbiont bacteria is unexplored. Therefore, we designed and conducted a study to identify bacterial isolates obtained from sponges. For this, we collected sponges samples (Hyrtios erectus, Clathria (Thalysias) reinwardti), Niphates sp., and Callyspongia sp.) from the Spermonde islands in Indonesia. We successfully found eight bacterial isolates from four sponges, as molecular identification based on 16S rRNA approach revealed bacterial isolates of SpAB1, SpAB2, SpBB1, SpDB1, and SpDB2 from three sponges (Hyrtios erectus, Clathria (Thalysias) reinwardti), Niphates sp.). Interestingly, these were closely related to Pseudomonas, and a bacterial isolate from Callyspongia sp. (SpCB1) showed similarity to Bacillus. Bacillus and Pseudomonas bacteria isolated from hydrocarbon-contaminated sponges exhibited degradation of naphthalene and pyrene PAHs.
... Culture-independent, as well as culture-dependent studies revealed that sponges have diverse bacterial populations. Phylogenetic studies clearly showed more than taxa belonging to thirty different bacterial phyla (Schleifer 2004;Webster et al. 2008;Sipkema et al. 2009), including the candidate phylum 'Poribacteria' (exclusively found within sponges; Fieseler et al. 2004;Lafi et al. 2009) are associated with sponges. ...
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... This becomes apparent by striking examples such as Pseudoalteromonas luteoviolacea's contractile injection system injecting tubeworms metamorphosis factors into host cells (Ericson et al., 2019, Shikuma et al., 2014, or even basic mechanisms of sporulation (Khanna et al., 2019), which, functionally, would have been hardly understood by genomic evidence alone. CHAPTER 3 provided the first clear evidence that supports the long standing hypothesis of cell compartmentation (Fieseler et al., 2004 in a lineage of sponge endemic Poribacteria (Podell et al., 2019, Steinert et al., 2018a, Lafi et al., 2009. This revealed that the poribacterial cell structure is more complex than previously thought. ...
Thesis
Holobionts result from intimate associations of eukaryotic hosts and microbes and are now widely accepted as ubiquitous and important elements of nature. Marine sponge holobionts combine simple morphology and complex microbiology whilst diverging early in the animal kingdom. As filter feeders, sponges feed on planktonic bacteria, but also harbour stable species-specific microbial consortia. This interaction with bacteria renders sponges to exciting systems to study basal determinants of animal-microbe symbioses. While inventories of symbiont taxa and gene functions continue to grow, we still know little about the symbiont physiology, cellular interactions and metabolic currencies within sponges. This limits our mechanistic understanding of holobiont stability and function. Therefore, this PhD thesis set out to study the questions of what individual symbionts actually do and how they interact. The first part of this thesis focuses on the cell physiology of cosmopolitan sponge symbionts. For the first time, I characterised the ultrastructure of dominant sponge symbiont clades within sponge tissue by establishing fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM). In combination with genome-centred metatranscriptomics, this approach revealed structural adaptations of symbionts to process complex holobiont-derived nutrients (i.e., bacterial microcompartments and bipolar storage polymers). Next, we unravelled complementary symbiont physiologies and cell co-localisation indicating vivid symbiont-symbiont metabolic interactions within the holobiont. This suggests strategies of nutritional resource partitioning and syntrophy to dominate over spatial segregation to avoid competitive exclusion- a mechanistic framework to sustain high microbial diversity. By combining stable isotope pulse-chase experiments with metabolic imaging, we demonstrated that symbionts can account for up to 60 % of the heterotrophic carbon and nitrogen assimilation in sponges. Thus, sponge symbiont action determines sponge-driven biochemical cycles in marine ecosystems. Finally, I explored the role of phages in the sponge holobiont focussing on tripartie phage-microbe-host interplay. Sponges appeared as rich reservoirs of novel viral diversity with 491 previously unidentified genus-level viral clades. Further, sponges harboured highly individual, yet species-specific viral communities. Importantly, I discovered that phages, termed “Ankyphages”, abundantly encode ankyrin proteins. Such “Ankyphages” I found to be widespread in host-associated environments, including humans. Using macrophage infection assays I showed that phage ankyrins aid bacteria in eukaryote immune evasion by downregulating eukaryotic antibacterial immunity. Thus, I identified a potentially widespread mechanism of tripartite phage-prokaryote-host interplay where phages foster animal-microbe symbioses. Altogether, I draw three main conclusions: The sponge holobiont is a metabolically intertwined ecosystem, with symbiont action impacting the environment, and tripartite phage-prokaryote-eukaryote interplay fostering symbiosis.
... Chemoautotrophs such as nitrifying archaea, bacteria and mixotrophic Poribacteria have a cosmopolitan distribution in sponges and the genomic repertoire for chemotrophy (Preston et al. 1996;Hallam et al. 2006;Taylor et al. 2007;Lafi et al. 2009;Siegl et al. 2011;Simister et al. 2012;Cardoso et al. 2013;Li et al. 2014). They fix inorganic carbon by obtaining the energy from the oxidation of reduced inorganic compounds e.g. ...
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Chapter
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Chapter
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