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Applied and Environmental Microbiology, April 2006, p. 3079-3083, Vol. 72, No. 4
0099-2240/06/$08.00+0 doi:10.1128/AEM.72.4.3079-3083.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Diversity and Distribution of Planctomycetes and Related Bacteria in the Suboxic Zone of the Black Sea
John Kirkpatrick,1
Brian Oakley,2
Clara Fuchsman,1
Sujatha Srinivasan,2
James T. Staley,2* and
James W. Murray1
School of Oceanography,1
Department of Microbiology, University of Washington, Seattle, Washington2
Received 19 September 2005/
Accepted 10 February 2006

ABSTRACT
Samples from six depths of the Black Sea's suboxic zone were
analyzed for 16S rRNA gene sequence information. A gradient
in phylotype diversity was found. The distributions of known
anaerobic
ammonium
oxidation (anammox) bacteria, many unknown
Planctomycetes, and other phylotypes were examined in relation
to the local nutrient and redox conditions.

INTRODUCTION
The Black Sea is the world's largest permanent anoxic basin
and is an excellent analog for early-Earth oceans (
1) and modern-day
oxygen-limited systems. Bacteria belonging to the phylum
Planctomycetes that can produce N
2 gas from NO
2 and NH
4+, i.e.,
anaerobic
ammonium
oxidation (anammox) bacteria, were recently identified
in the suboxic zone here (
13). This recently discovered N cycle
pathway has been estimated to account for between one-fifth
(
5) and essentially all (
14) of the N
2 production in marine
oxygen-minimal zones. All known anammox bacteria belong to the
bacterial phylum
Planctomycetes (
3,
10); their activity has
also been reported to occur in wastewater treatment facilities
(
30), marine sediments (
31), and sea ice (
22).
Planctomycetes are characterized by intracellular membranes (sometimes enclosing condensed nuclei [17]), reproductive budding, a lack of peptidoglycan, and a wide distribution (8, 9). Interestingly, ether- and ester-linked lipids (6), a sterol production pathway (21), and C1 transfer genes phylogenetically intermediate between Archaea and Proteobacteria (3) have all been found in this phylum. The genera Planctomyces, Gemmata, Isosphaera, Pirellula, Blastopirellula, and Rhodopirellula are known from pure culture (28). Discovery and cultivation of anammox bacteria has resulted in the recognition of "Candidatus" genera "Brocadia," "Kuenenia," and "Scalindua" (25, 26, 27, 30).
The aim of this study was to elucidate the composition of Planctomycetes in the Black Sea in order to shed some light on this intriguing phylum, as the complete extent of its diversity, distribution, and metabolic potential remains unknown. The first task undertaken was to obtain and assess detailed 16S rRNA gene sequence information about the planctomycetes which reside in the suboxic zone. The second was to apply this information to concurrent chemical data to better understand how the community structure relates to natural abundances of different N species.

Sample collection.
Samples were obtained in April 2003 onboard the R/V
Knorr from
the Black Sea's central gyre (42'30.79'' N, 30'59.60'' E) by
use of a conductivity-temperature-depth Rosette with SeaBird
sensors. Two liters of seawater for DNA extraction was pressure
filtered from Niskin bottles onto 0.2-µm Millipore Sterivex
filters and frozen.

Chemical data.
Nutrient samples were analyzed onboard using a two-channel Technicon
Autoanalyzer II. Nitrite, nitrate, and ammonia were measured
as described elsewhere (
2,
28). Oxygen and hydrogen sulfide
samples were measured with wet chemical and polarographic techniques
by S. Konovalov and A. Romanov (Marine Hydrophysical Institute,
Sevastopol, Ukraine). A complete chemical analysis is provided
elsewhere (
18a).

DNA extraction and analysis.
DNA was extracted from filters as described elsewhere (
34).
Samples were PCR amplified for partial 16S rRNA gene sequencing
by using
Planctomycetes-specific primers 58f (5'-GGCATGGATTAGGCATGC-3')
(
16) and 926r (5'-CCACCGCTTGTGTGAGCCCC-3') (
35) for 32 cycles
with an annealing temperature of 60°C. PCR products were
cloned and sequenced with standard methods (see, e.g., reference
23). Sequences were edited, aligned, and analyzed for tree construction
and rarefaction analysis with the following programs: Sequencher
(
http://www.genecodes.com), ClustalX (
32), Genedoc (
20), Bellerophon
(
12), RDP's CHECK_CHIMERA (
4), TreeCon (
33), Phylip (
http://evolution.genetics.washington.edu/phylip.html),
and DOTUR (
24).

Chemical profiles.
The suboxic zone of the Black Sea is defined by low oxygen (<10
µM) and H
2S (<10 nM) concentrations. At the time of
sampling, suboxic conditions were found between


of 15.59 (approximately
53 m) and


of 16.01 (approximately 69 m), where sulfide was
first detectable (Fig.
1a). Although the absolute depth may
change (
18), the density stratification creates a stable region
where NO
3 and NH
4+ are completely consumed (Fig.
1b),
and thus depth is given in density units (


) rather than meters.

Diversity of Planctomycetes and related organisms.
Three hundred thirty complete insert sequences from six depths
defined 56 unique operational taxonomic units (OTUs) by use
of the furthest-neighbor approach with a 97% sequence similarity
cutoff (Table
1; Fig.
2). The primer set utilized proved effective
in selecting for many unknown
Planctomycetes sequences, although
non-
Planctomycetes phylotypes were also amplified. Eleven distinct
groups were defined (Fig.
2 and
3). Four of these groups were
clearly
Planctomycetes:
Pirellula (group A),
Planctomyces spp.
(group B), unknown
Planctomycetes/BO84 sequence type (from enrichment
culture [unpublished data]) (group C), and known anammox bacteria
(group D).
Chlamydia (group E) was represented by a single sequence
but shared subdivision/division level affiliation with a larger
unknown group (group F), found throughout the suboxic zone but
with some genus-level depth specificity.
Several phylotypes were found for
Verrucomicrobia (group G)
and a single sequence for
Lentisphaerae (group H). Some other
non-
Planctomycetes sequences appear more derived, such as candidate
division OD1 (group I), although they are not closely related
(

80% similarity) to previously sampled organisms. The greatest
diversity of this group is found deep in the suboxic zone, near
the onset of sulfide. Despite their phylogenetic divergence,
organisms in this group may be involved in sulfur cycling, consistent
with previous observations of the candidate division OD1 (
11).
Note that the new OD1 sequences obtained have a 100% sequence
identity with the probe PLA46 (
19), originally designed for
the
Planctomycetes. Another uncultured group (group J) is apparently
related to candidate division OP3. Group K appears deep in the
suboxic zone and expands the known diversity of candidate division
WS3. Representatives of this group, originally discovered in
a methanogenic aquifer (
7), are absent at shallower depths (Fig.
3). The most similar known sequences (similarity of 73 to 89%)
are salt marsh sediment clones.

Anammox bacteria.
"
Candidatus Scalindua sorokinii" is the only known marine anammox
bacterium and has been previously reported from the Black Sea
(
13,
27,
30). It was found at most depths, except


of 15.5 and
15.7. NO
2 and NH
4+ overlapped at the lowest depths; however,
"
Candidatus Scalindua sorokinii" sequences dominated clone libraries
at the intermediate depth of


of 15.8 (Fig.
3 and
4b). It is
curious that bacteria at this depth were separated from the
upward flux of NH
4+ from depth. NH
4+ was not measurable until
multiple layers deeper in the suboxic zone (


> 15.90), where
a different community structure is found. This can be explained
several ways: (i) some proportion of anammox activity may rely
on remineralization of NH
4+ from organic matter, which is consistent
with natural nitrogen isotope ratios in the Black Sea (
18a),
(ii) interspecies NH
4+ transfer could be supplying this substrate
for anammox bacteria, or (iii) the "
Candidatus Scalindua"-type
sequences found at middle and upper depths may represent inactive
bacteria.

Overall diversity.
Clone library diversity varied greatly between the different
density layers (Fig.
3 and
4). Libraries from the shallow to
intermediate depths returned fewer OTUs and tended to be dominated
by a few sequences, such as "
Candidatus Scalindua" or the BO84
type. Deeper areas of the suboxic zone (


= 15.9 and


= 16.0)
exhibited a broad array of highly divergent sequences, as reflected
in rarefaction curves; the six different densities sampled show
two distinct patterns (Fig.
4). Clone libraries from the bottom
two depths, where nitrate is absent and ammonium and sulfide
begin to permeate into the suboxic zone, had a steeper rarefaction
curve. The relative taxonomic richness here is in part due to
the presence of deeply branching groups such as OD1 (Fig.
2 and
3). Even when the data set is restricted to "true"
Planctomycetes sequences (Fig.
4b), however, lower depths appear to harbor
a greater diversity of bacteria than the more oxidized upper
layers.
Overall, there were marked differences in community structure between as little as 0.1 density units (typically 2 or 3 m here). Depths which had measurable levels of nitrate had lower diversity, both in the overall number of unique OTUs and in their relatedness to each other (Table 1; Fig. 3 and 4). When nitrate decreases and there is a transition to a more reducing environment (
= 15.9 and 
= 16.0), there is a notable increase in the overall number of OTUs and a decrease in their relatedness to each other. This was mainly due to the presence of uncultured organisms related to candidate divisions OD1 and WS3, but Planctomycetes sequences contribute to this effect. It has long been noted that transition zones or ecotones such as these can host high levels of diversity (see, e.g., references 15 and 29); the suboxic-zone sequences are consistent with these observations. Further work is needed, however, to characterize the unknown bacteria found here and to detail their significance to biogeochemical cycling.

Nucleotide sequence accession numbers.
Nucleotide sequence accession numbers in the GenBank database
are DQ368063 to DQ368333.

ACKNOWLEDGMENTS
We are grateful to William Brazelton, David Stahl, Cheryl Jenkins,
and the R/V
Knorr crew for their help.
This work was funded by NSF Microbial Observatories grant MCB-0132101 and NSF-IGERT grant DGE-9870713 for astrobiology.

FOOTNOTES
* Corresponding author. Mailing address: University of Washington, Department of Microbiology, Box 357242, Seattle, WA 98195. Phone: (206) 543-0461. Fax: (206) 543-8297. E-mail:
jtstaley{at}u.washington.edu.


REFERENCES
1 - Anbar, A. D., and A. H. Knoll. 2002. Proterozoic ocean chemistry and evolution: a bioinorganic bridge? Science 297:1137-1142.[CrossRef][Medline]
2 - Armstrong, F. A., C. R. Stearns, and J. D. H. Strickland. 1967. The measurement of upwelling and subsequent biological processes by means of the Technicon AutoAnalyzer and associated equipment. Deep-Sea Res. 14:381-389.
3 - Chistoserdova, L., C. Jenkins, M. G. Kalyuzhnaya, C. J. Marx, A. Lapidus, J. A. Vorholt, J. T. Staley, and M. E. Lidstrom. 2004. The enigmatic planctomycetes may hold a key to the origins of methanogenesis and methylotrophy. Mol. Biol. Evol. 21:1234-1241.[Abstract/Free Full Text]
4 - Cole, J. R., B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kulam, S. Chandra, D. M. McGarrell, T. M. Schmidt, G. M. Garrity, and J. M. Tiedje. 2003. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31:442-443.[Abstract/Free Full Text]
5 - Dalsgaard, T., D. E. Canfield, J. Petersen, B. Thamdrup, and J. Acuña-González. 2003. N2 production by the anammox reaction in the anoxic water column of Golfo Dulce, Costa Rica. Nature 422:606-608.[CrossRef]
6 - Damsté, J. S. S., M. Strous, W. I. C. Rijpstra, E. C. Hopmans, J. A. J. Geenevasen, A. C. T. van Duin, L. A. van Niftrik, and M. S. M. Jetten. 2002. Linearly concatenated cyclobutane lipids form a dense bacterial membrane. Nature 419:708-712.[CrossRef][Medline]
7 - Dojka, M. A., P. Hugenholtz, S. K. Haack, and N. R. Pace. 1998. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64:3869-3877.[Abstract/Free Full Text]
8 - Fuerst, J. A. 1995. The planctomycetes: emerging models for microbial ecology, evolution and cell biology. Microbiology 141:1493-1506.[Free Full Text]
9 - Fuerst, J. A., H. G. Gwilliam, M. Lindsay, A. Lichanska, C. Belcher, J. E. Vickers, and P. Hugenholtz. 1997. Isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, Penaeus monodon. Appl. Environ. Microbiol. 63:254-262.[Abstract]
10 - Fuerst, J. A. 2005. Intracellular compartmentation in planctomycetes. Annu. Rev. Microbiol. 59:299-328.[CrossRef][Medline]
11 - Harris, J. K., S. T. Kelley, and N. R. Pace. 2004. New perspective on uncultured bacterial phylogenetic division OP11. Appl. Environ. Microbiol. 70:845-849.[Abstract/Free Full Text]
12 - Huber, T., G. Faulkner, and P. Hugenholtz. 2004. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317-2319.[Abstract/Free Full Text]
13 - Kuypers, M. M. M., A. O. Sliekers, G. Lavik, M. Schmid, B. B. Jørgensen, J. G. Kuenen, J. S. Sinninghe Damsté, M. Strous, and M. S. M. Jetten. 2003. Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422:608-611.[CrossRef]
14 - Kuypers, M. M. M., G. Lavik, D. Woebken, M. Schmid, B. M. Fuchs, R. Amann, B. B. Jørgensen, and M. S. M. Jetten. 2005. Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc. Natl. Acad. Sci. USA 102:6478-6483.[Abstract/Free Full Text]
15 - Lachavanne, J.-B., and R. Juge. 1997. Land-inland water ecotones as transitional systems of particularly high biodiversity: towards a synthesis, p. 277-297. In J.-B. Lachavanne and R. Juge (ed.), Biodiversity in land-inland water ecotones. UNESCO, Paris, France.
16 - Liesack, W., and E. Stackebrandt. 1992. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J. Bacteriol. 174:5072-5078.[Abstract/Free Full Text]
17 - Lindsay, M. R., R. I. Webb, M. Strous, M. S. M. Jetten, M. K. Butler, R. J. Forde, and J. A. Fuerst. 2001. Cell compartmentalization in planctomycetes: novel types of structural organization for the bacterial cell. Arch. Microbiol. 175:413-429.[CrossRef][Medline]
18 - Murray, J. W., L. A. Codispoti, and G. E. Friederich. 1995. Oxidation-reduction environments: the suboxic zone in the Black Sea, p. 157-176. In C. P. Huang, C. O'Melia, and J. J. Morgan (ed.), Aquatic chemistry. American Chemical Society, Washington, D.C.
18 - Murray, J. W., C. Fuchsman, J. Kirkpatrick, B. Paul, and S. K. Konovalov. 2005. Species and
15N signatures of nitrogen transformations in the suboxic zone of the Black Sea. Oceanography 18:36-47. 19 - Neef, A., R. Amann, H. Schlesner, and K.-H. Schleifer. 1998. Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes. Microbiology 144:3257-3266.[Abstract/Free Full Text]
20 - Nicholas, K. B., H. B. Nicholas, Jr., and D. W. Deerfield II. 31 July 1997, posting date. GeneDoc: analysis and visualization of genetic variation. EMBnet.news 4. [Online.] http://www.ebi.ac.uk/embnet.news/vol4_2/genedoc.html.
21 - Pearson, A., M. Budin, and J. J. Brocks. 2003. Phylogenetic biochemical evidence for sterol synthesis in the bacterium Gemmata obscuriglobus. Proc. Natl. Acad. Sci. USA 100:15352-15357.[Abstract/Free Full Text]
22 - Rysgaard, S., and R. N. Glud. 2004. Anaerobic N2 production in Arctic sea ice. Limnol. Oceanogr. 49:86-94.
23 - Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
24 - Schloss, P. D., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.[Abstract/Free Full Text]
25 - Schmid, M., S. Schmitz-Esser, M. Jetten, and M. Wagner. 2001. 16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection. Environ. Microbiol. 3:450-459.[CrossRef][Medline]
26 - Schmid, M., K. Walsh, R. Webb, W. I. C. Rijpstra, K. van de Pas-Schoonen, M. J. Verbruggen, T. Hill, B. Moffett, J. Fuerst, S. Schouten, J. S. Sinninghe Damsté, J. Harris, P. Shaw, M. Jetten, and M. Strous. 2003. Candidatus "Scalindua brodae", sp. nov., Candidatus "Scalindua wagneri", sp. nov., two new species of anaerobic ammonium oxidizing bacteria. Syst. Appl. Microbiol. 26:529-538.[CrossRef][Medline]
27 - Schmid, M., U. Twachtmann, M. Klein, M. Strous, S. Juretschko, M. Jetten, J. W. Metzger, K.-H. Schleifer, and M. Wagner. 2000. Molecular evidence for genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation. Syst. Appl. Microbiol. 23:93-106.[Medline]
28 - Slawyk, G., and J. J. MacIsaac. 1972. Comparison of two automated ammonium methods in a region of coastal upwelling. Deep-Sea Res. 19:521-524.
29 - Smith, T. B., S. Kark, C. J. Schneider, R. K. Wayne, and C. Moritz. 2001. Biodiversity hotspots and beyond: the need for preserving environmental transitions. Trends Ecol. Evol. 16:431.
30 - Strous, M., J. A. Fuerst, E. H. M. Kramer, S. Logemann, G. Muyzer, K. T. van de Pas-Schoonen, R. Webb, J. Gijs Kuenen, and M. S. M. Jetten. 1999. Missing lithotroph identified as new planctomycete. Nature 400:446-449.[CrossRef][Medline]
31 - Thamdrup, B., and T. Dalsgaard. 2002. Production of N2 through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments. Appl. Environ. Microbiol. 68:1312-1318.[Abstract/Free Full Text]
32 - Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.[Abstract/Free Full Text]
33 - Van de Peer, Y., and R. De Wachter. 1997. Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Comput. Appl. Biosci. 13:227-230.[Abstract/Free Full Text]
34 - Vetriani, C., H. V. Tran, and L. J. Kerkhof. 2003. Fingerprinting microbial assemblages from the oxic/anoxic chemocline of the Black Sea. Appl. Environ. Microbiol. 69:6481-6488.[Abstract/Free Full Text]
35 - Wang, J., C. Jenkins, R. I. Webb, and J. A. Fuerst. 2002. Isolation of Gemmata-like and Isosphaera-like bacteria from soil and freshwater. Appl. Environ. Microbiol. 68:417-422.[Abstract/Free Full Text]
Applied and Environmental Microbiology, April 2006, p. 3079-3083, Vol. 72, No. 4
0099-2240/06/$08.00+0 doi:10.1128/AEM.72.4.3079-3083.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
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