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Supplementary Table S1: Selected genomic and metagenomic data of marine Planctomycetia and other clades. mb: metagenomic bin; scg: single cell genome; g: genome;

*: according to phylogenetic reconstruction of Planctomycetes (Chapter I Figure 4).

Product ID Phylogeny Source Reference

mb P1 Planctomycetia algae (Kim et al., 2016a)

mb P2 Planctomycetia;

Rhodopirellula algae (Kim et al., 2016a)

mb P3 Planctomycetia algae (Kim et al., 2016a)

mb SM23-65 Planctomycetes sediment (Baker et al., 2015) mb SM23-32 Planctomycetes sediment (Baker et al., 2015) mb SM23-25 Planctomycetes sediment (Baker et al., 2015) mb DG-58 Plantomycetes sediment (Baker et al., 2015) mb DG-23 Plantomycetes sediment (Baker et al., 2015) mb DG-20 Plantomycetes sediment (Baker et al., 2015) mb SM23-33 Plantomycetes sediment (Baker et al., 2015) mb SM23-30 Plantomycetes sediment (Baker et al., 2015) mb SM1-79 Plantomycetes sediment (Baker et al., 2015) mb SG8-4 Plantomycetes sediment (Baker et al., 2015) mb Planctomycetales bacterium

4572_13 Planctomycetia sediment (Dombrowski et al., 2017) mb Planctomycetales bacterium

4484_113 Planctomycetia sediment (Dombrowski et al., 2017) mb Planctomycetales bacterium

4484_123 Planctomycetia sediment (Dombrowski et al., 2017) mb Planctomycetales bacterium

71-10 Planctomycetia sediment (Dombrowski et al., 2017) mb bacterium BBD 1991-11 Planctomycetia water Den Uyl, P.A (…) Dick, G.J.,

unpublished scg Planctomycetes bacterium

SCGC AAA282-C1 Planctomycetia water DOE JGI, unpublished

mb bin3 Planctomycetia algae (Vollmers et al., 2017)

mb bin4 Planctomycetia algae (Vollmers et al., 2017)

mb bin5 Planctomycetia algae (Vollmers et al., 2017)

mb bin6 Planctomycetia algae (Vollmers et al., 2017)

mb bin7 Planctomycetia algae (Vollmers et al., 2017)

mb bin8 Planctomycetia algae (Vollmers et al., 2017)

mb Lau35 Pla3 lineage plume (Anantharaman et al., 2016) mb Lau36 Pla3 lineage plume (Anantharaman et al., 2016) mb Lau94 Planctomycetia plume (Anantharaman et al., 2016)

mb Bin62 Planctomycetia;

Blastopirellula-related* plume (Li et al., 2016)

mb Bin102 Planctomycetia;

Rhodopirellula/

Rubpripirellula*

plume (Li et al., 2016)

mb Bin39 Planctomycetia;

Planctomyces* plume (Li et al., 2016)

mb Bin64 OM190* plume (Li et al., 2016)

mb Bin53 OM190* plume (Li et al., 2016)

General Conclusion and Outlook: Appendix

168

mb Bin81 Pla3 lineage* plume (Li et al., 2016)

mb TARA_PSW_MAG_00018 Planctomycetia water (Delmont et al., 2017) mb TARA_PSW_MAG_00130 Planctomycetia water (Delmont et al., 2017) mb TARA_ANE_MAG_00062 Planctomycetia water (Delmont et al., 2017) mb TARA_ANE_MAG_00081 Planctomycetia water (Delmont et al., 2017) mb TARA_ANW_MAG_00007 Planctomycetia water (Delmont et al., 2017) mb TARA_ANW_MAG_00014 Planctomycetia water (Delmont et al., 2017) mb TARA_ANW_MAG_00022 Planctomycetia;

Planctomyces water (Delmont et al., 2017) mb TARA_ANW_MAG_00035 Planctomycetia water (Delmont et al., 2017) mb TARA_ANW_MAG_00039 Planctomycetia water (Delmont et al., 2017) mb TARA_ANW_MAG_00077 Planctomycetia water (Delmont et al., 2017) mb TARA_ASE_MAG_00028 Planctomycetia water (Delmont et al., 2017) mb TARA_ION_MAG_00007 Planctomycetia water (Delmont et al., 2017) mb TARA_IOS_MAG_00034 Planctomycetia water (Delmont et al., 2017) mb TARA_IOS_MAG_00049 Planctomycetia water (Delmont et al., 2017) mb TARA_MED_MAG_00126 Planctomycetia water (Delmont et al., 2017) mb TARA_PON_MAG_00068 Planctomycetia water (Delmont et al., 2017) mb TARA_PSE_MAG_00023 Planctomycetia water (Delmont et al., 2017) mb TARA_PSE_MAG_00028 Planctomycetia water (Delmont et al., 2017) mb TARA_PSE_MAG_00058 Planctomycetia water (Delmont et al., 2017) mb TARA_PSE_MAG_00066 Planctomycetia water (Delmont et al., 2017) mb TARA_PSE_MAG_00082 Planctomycetia water (Delmont et al., 2017) mb TARA_PSE_MAG_00089 Planctomycetia water (Delmont et al., 2017) mb TARA_PSE_MAG_00095 Planctomycetia water (Delmont et al., 2017) mb TARA_PSE_MAG_00097 Planctomycetia;Planctomyces water (Delmont et al., 2017) mb TARA_PSE_MAG_00112 Planctomycetia water (Delmont et al., 2017) mb TARA_PSE_MAG_00125 Planctomycetia water (Delmont et al., 2017) mb TARA_PSE_MAG_00141 Planctomycetia water (Delmont et al., 2017) mb TARA_PSW_MAG_00023 Planctomycetia water (Delmont et al., 2017) mb TARA_PSW_MAG_00027 Planctomycetia water (Delmont et al., 2017) mb TARA_PSW_MAG_00072 Planctomycetia water (Delmont et al., 2017) mb TARA_PSW_MAG_00097 Planctomycetia water (Delmont et al., 2017) mb TARA_PSW_MAG_00110 Planctomycetia water (Delmont et al., 2017) mb TARA_PSW_MAG_00113 Planctomycetia water (Delmont et al., 2017) mb TARA_PSW_MAG_00122 Planctomycetia water (Delmont et al., 2017) mb TARA_PSW_MAG_00123 Planctomycetia water (Delmont et al., 2017) mb TARA_PSW_MAG_00127 Planctomycetia water (Delmont et al., 2017) mb TARA_RED_MAG_00020 Planctomycetia;Planctomyces water (Delmont et al., 2017) mb TARA_RED_MAG_00036 Planctomycetia;Planctomyces water (Delmont et al., 2017) mb TARA_RED_MAG_00050 Planctomycetia;Planctomyces water (Delmont et al., 2017) mb TARA_RED_MAG_00078 Planctomycetia water (Delmont et al., 2017) mb TARA_RED_MAG_00093 Planctomycetia water (Delmont et al., 2017) mb TARA_RED_MAG_00100 Planctomycetia water (Delmont et al., 2017) mb TARA_RED_MAG_00115 Planctomycetia water (Delmont et al., 2017)

g Planctomycetia; Fuerstia

marisgermanicae crustacean

shell (Kohn et al., 2016)

g Blastopirellula marina

DSM3645 water (Schlesner et al., 2004), Gordon Betty More Foundation, direct submission

General Conclusion and Outlook: Appendix

g Planctomyces maris

DSM8797 water (Bauld and Staley, 1976), Amann, R (…) Venter, J. (2007) C. direct

submission

g Rhodopirellula baltica SH 1 water (Glöckner et al., 2003; Schlesner et al., 2004)

g Rhodopirellula baltica

SH 28 water (Schlesner et al., 2004; Richter et al., 2014a)

g Rhodopirellula baltica

SWK 14 algae (Winkelmann and Harder, 2009;

Richter et al., 2014a)

g Rhodopirellula baltica

WH 47 sediment (Winkelmann and Harder, 2009;

Richter et al., 2014a)

g Rhodopirellula europaea

6C water (Winkelmann and Harder, 2009;

Richter-Heitmann et al., 2014)

g Rhodopirellula europaea

SH398C water (Schlesner et al., 2004; Richter-Heitmann et al., 2014)

g Rhodopirellula maiorica

SM 1 sediment (Winkelmann and Harder, 2009;

Richter et al., 2014b)

g Rhodopirellula sallentina

SM 41 sediment/water (Schlesner et al., 2004; Wegner et al., 2014)

g Rhodopirellula rubra.

SWK7 algae (Winkelmann and Harder, 2009;

Klindworth et al., 2014a)

g Rhodopirellula islandica

K833 water (Winkelmann and Harder, 2009;

Kizina et al., 2015)

References

170

References

Acosta-González, A., Rosselló-Móra, R., and Marqués, S. (2013) Characterization of the anaerobic microbial community in oil-polluted subtidal sediments: aromatic biodegradation potential after the Prestige oil spill. Environ Microbiol 15: 77-92.

Ahmerkamp, S., Winter, C., Krämer, K., Beer, D.d., Janssen, F., Friedrich, J. et al. (2017) Regulation of benthic oxygen fluxes in permeable sediments of the coastal ocean. Limnol Oceanogr: doi: 10.1002/lno.10544.

Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K.L., Tyson, G.W., and Nielsen, P.H. (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31: 533-538.

Alderkamp, A.C., van Rijssel, M., and Bolhuis, H. (2007) Characterization of marine bacteria and the activity of their enzyme systems involved in degradation of the algal storage glucan laminarin. FEMS Microbiol Ecol 59: 108-117.

Aller, R.C. (1978) The effects of animal-sediment interactions on geochemical processes near the sediment-water interface. In Estuarine Interactions. Wiley, M.L. (ed). New York:

Academic Press, pp. 157-172.

Amann, R.I., Ludwig, W., and Schleifer, K.-H. (1995) Phylogenetic identification and in situ detection of individual microbial-cells without cultivation. Microbiol Rev 59: 143-169.

Amann, R.I., Binder, B.J., Olson, R.J., Chisholm, S.W., Devereux, R., and Stahl, D.A. (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56: 1919-1925.

Andreote, F.D., Jimenez, D.J., Chaves, D., Dias, A.C.F., Luvizotto, D.M., Dini-Andreote, F.

et al. (2012) The microbiome of brazilian mangrove sediments as revealed by metagenomics. PloS One 7: e38600.

Arndt, S., Jørgensen, B.B., LaRowe, D.E., Middelburg, J.J., Pancost, R.D., and Regnier, P.

(2013) Quantifying the degradation of organic matter in marine sediments: A review and synthesis. Earth-Sci Rev 123: 53-86.

Arnosti, C. (2004) Speed bumps and barricades in the carbon cycle: substrate structural effects on carbon cycling. Mar Chem 92: 263-273.

Asami, H., Aida, M., and Watanabe, K. (2005) Accelerated sulfur cycle in coastal marine sediment beneath areas of intensive shellfish aquaculture. Appl Environ Microbiol 71:

2925-2933.

Azam, F., Fenchel, T., Field, J.G., Gray, J.S., Meyer-Reil, L.-A., and Thingstad, F. (1983) The ecological role of water-column microbes in the sea. Mar Ecol Prog Ser 10: 257-263.

Bacci, G., Pagoto, E., Passaponti, M., Vannocci, P., Ugolini, A., and Mengoni, A. (2015) Composition of supralittoral sediments bacterial communities in a Mediterranean island.

Ann Microbiol 65: 1-13.

Bailey, V.L., Fansler, S.J., Stegen, J.C., and McCue, L.A. (2013a) Linking microbial community structure to ȕ-glucosidic function in soil aggregates. ISME J 7: 2044-2053.

Bailey, V.L., McCue, L.A., Fansler, S.J., Boyanov, M.I., DeCarlo, F., Kemner, K.M., and Konopka, A. (2013b) Micrometer-scale physical structure and microbial composition of soil macroaggregates. Soil Biol Biochem 65: 60-68.

References

Bak, F., and Cypionka, H. (1987) A novel type of energy metabolism involving fermentation of inorganic sulphur compounds. Nature 326: 891-892.

Bak, F., Finster, K., and Rothfuß, F. (1992) Formation of dimethylsulfide and methanethiol from methoxylated aromatic compounds and inorganic sulfide by newly isolated anaerobic bacteria. Arch Microbiol 157: 529-534.

Baker, B.J., Lazar, C.S., Teske, A.P., and Dick, G.J. (2015) Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria.

Microbiome 3:14.

Bakunina, I., Nedashkovskaya, O., Balabanova, L., Zvyagintseva, T., Rasskasov, V., and Mikhailov, V. (2013) Comparative analysis of glycoside hydrolases activities from phylogenetically diverse marine bacteria of the genus Arenibacter. Mar Drugs 11: 1977-1998.

Bakunina, I.Y., Nedashkovskaya, O.I., Kim, S.B., Zvyagintseva, T.N., and Mikhailov, V.V.

(2012) Distribution of Į-N-acetylgalactosaminidases among marine bacteria of the phylum Bacteroidetes, epiphytes of marine algae of the Seas of Okhotsk and Japan. Microbiol 81:

373-378.

Bakunina, I.Y., Kuhlmann, R.A., Likhosherstov, L.M., Martynova, M.D., Nedashkovskaya, O.I., Mikhailov, V.V., and Elyakova, L.A. (2002) Į-N-acetylgalactosaminidase from marine bacterium Arenibacter latericius KMM 426(T) removing blood type specificity of A-erythrocytes. Biochemistry(Moscow) 67: 689-695.

Bear, J. (1972) Dynamics of fluids in porous media. New York: Elsevier Publishing Company, Int.

Becker, G.A., Dick, S., and Dippner, J.W. (1992) Hydrography of the German Bight. Mar Ecol Prog Ser 91: 9-18.

Beier, S., Rivers, A.R., Moran, M.A., and Obernosterer, I. (2014) The transcriptional response of prokaryotes to phytoplankton-derived DOM in seawater. Environ Microbiol 17: 3466-3480.

Béjà, O., Aravind, L., Koonin, E.V., Suzuki, M.T., Hadd, A., Nguyen, L.P. et al. (2000) Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science 289: 1902-1906.

Bengtsson, M.M., and Øvreås, L. (2010) Planctomycetes dominate biofilms on surfaces of the kelp Laminaria hyperborea. BMC Microbiol 10:261: 1-12.

Bjursell, M.K., Martens, E.C., and Gordon, J.I. (2006) Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. J Biol Chem 281: 36269-36279.

Boedeker, C., Schuler, M., Reintjes, G., Jeske, O., van Teeseling, M.C.F., Jogler, M. et al.

(2017) Determining the bacterial cell biology of Planctomycetes. Nat Commun 8: doi:

10.1038/ncomms14853.

Böer, S.I., Arnosti, C., van Beusekom, J.E.E., and Boetius, A. (2009) Temporal variations in microbial activities and carbon turnover in subtidal sandy sediments. Biogeosciences 6:

1149-1165.

Bollmann, A., Lewis, K., and Epstein, S.S. (2007) Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl Environ Microbiol 73:

6386-6390.

References

172

Bond, P.L., Hugenholtz, P., Keller, J., and Blackall, L.L. (1995) Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol 61: 1910-1916.

Bondoso, J., Albuquerque, L., Lobo-Da-Cunha, A., Da Costa, M.S., Harder, J., and Lage, O.M. (2014) Rhodopirellula lusitana sp. nov. and Rhodopirellula rubra sp. nov., isolated from the surface of macroalgae. Syst Appl Microbiol 37: 157-164.

Boon, A.R., Duineveld, G.C.A., Berghuis, E.M., and van der Weele, J.A. (1998) Relationships between benthic activity and the annual phytopigment cycle in near-bottom water and sediments in the southern North Sea. Estuarine Coastal Shelf Sci 46: 1-13.

Boudreau, B.P., Huettel, M., Forster, S., Jahnke, R.A., McLachlan, A., Middelburg, J.J. et al.

(2001) Permeable marine sediments: Overturning an old paradigm. Eos, Transactions American Geophysical Union 82: 133-136.

Bowman, J.P. (2006) The marine clade of the family Flavobacteriaceae: the genera Aequorivita, Arenibacter, Cellulophaga, Croceibacter, Formosa, Gelidibacter, Gillisia, Maribacter, Mesonia, Muricauda, Polaribacter, Psychroflexus, Psychroserpens, Robiginitalea, Salegentibacter, Tenacibaculum, Ulvibacter, Vitellibacter and Zobellia. In The Prokaryotes: Volume 7: Proteobacteria: Delta, Epsilon Subclass. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., and Stackebrandt, E. (eds). New York, NY:

Springer New York, pp. 677-694.

Bowman, J.P., and McCuaig, R.D. (2003) Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl Environ Microbiol 69: 2463-2483.

Bowman, J.P., McCammon, S.A., and Dann, A.L. (2005) Biogeographic and quantitative analyses of abundant uncultivated Ȗ-proteobacterial clades from marine sediment. Microb Ecol 49: 451-460.

Brinkhoff, T., Muyzer, G., Wirsen, C.O., and Kuever, J. (1999) Thiomicrospira chilensis sp.

nov., a mesophilic obligately chemolithoautotrophic sulfur-oxidizing bacterium isolated from a Thioplocamat. Int J Syst Bacteriol 49: 875-879.

Brinkhoff, T., Santegoeds, C.M., Sahm, K., Kuever, J., and Muyzer, G. (1998) A polyphasic approach to study the diversity and vertical distribution of sulfur-oxidizing Thiomicrospira species in coastal sediments of the German Wadden Sea. Appl Environ Microbiol 64:

4650-4657.

Brinkhoff, T., Fischer, D., Vollmers, J., Voget, S., Beardsley, C., Thole, S. et al. (2012) Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria.

ISME J 6: 1260-1272.

Brockhausen, I., Schachter, H., and Stanley, P. (2009) O-GalNAc Glycans. In Essentials of Glycobiology. Varki, A., Cummings, R.D., Esko, J.D., Freeze, H.H., Stanley, P., Bertozzi, C.R. et al. (eds). Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.

Brockmann, U.H., Laane, R.W.P.M., and Postma, H. (1990) Cycling of nutrient elements in the North Sea. Netherlands Journal of Sea Research 26: 239-264.

Buchan, A., LeCleir, G.R., Gulvik, C.A., and Gónzalez, J.M. (2014) Master recyclers:

features and functions of bacteria associated with phytoplankton blooms. Nat Rev Microbiol 12: 686-698.

Bühring, S.I., Elvert, M., and Witte, U. (2005) The microbial community structure of different permeable sandy sediments characterized by the investigation of bacterial fatty acids and fluorescence in situ hybridization. Environ Microbiol 7: 281-293.

References

Bühring, S.I., Ehrenhauss, S., Kamp, A., Moodley, L., and Witte, U. (2006) Enhanced benthic activity in sandy sublittoral sediments: Evidence from 13C tracer experiments. Mar Biol Res 2: 120-129.

Burdige, D.J., and Komada, T. (2015) Sediment pore waters In Biogeochemistry of Marine Dissolved Organic Matter Carlson, C.A. (ed). Boston: Academic Press, pp. 535-577.

Burdige, D.J., Kline, S.W., and Chen, W. (2004) Fluorescent dissolved organic matter in marine sediment pore waters. Mar Chem 89: 289-311.

Burke, C., Thomas, T., Lewis, M., Steinberg, P., and Kjelleberg, S. (2011) Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis. ISME J 5: 590-600.

Cahoon, L.B., and Safi, K.A. (2002) Distribution and biomass of benthic microalgae in Manukau Harbour, New Zealand. New Zeal J Mar Fresh 36: 257-266.

Canfield, D.E., Erik, K., and Bo, T. (2005a) Heterotrophic carbon metabolism. In Advances in Marine Biology. Donald E. Canfield, Kristensen, E., and Bo, T. (eds): Academic Press, pp.

129-166.

Canfield, D.E., Erik, K., and Bo, T. (2005b) The sulfur cycle. In Advances in marine biology:

Academic Press, pp. 313-381.

Cardman, Z., Arnosti, C., Durbin, A., Ziervogel, K., Cox, C., Steen, A.D., and Teske, A.

(2014) Verrucomicrobia are candidates for polysaccharide-degrading bacterioplankton in an arctic fjord of Svalbard. Appl Environ Microbiol 80: 3749-3756.

Carlson, C.A., Giovannoni, S.J., Hansell, D.A., Goldberg, S.J., Parsons, R., Otero, M.P. et al.

(2002) Effect of nutrient amendments on bacterioplankton production, community structure, and DOC utilization in the northwestern Sargasso Sea. Aquat Microb Ecol 30:

19-36.

Carvalhais, L.C., Dennis, P.G., Tyson, G.W., and Schenk, P.M. (2012) Application of metatranscriptomics to soil environments. J Microbiol Methods 91: 246-251.

Chen, J.W., Hanke, A., Tegetmeyer, H.E., Kattelmann, I., Sharma, R., Hamann, E. et al.

(2017) Impacts of chemical gradients on microbial community structure. ISME J 11: 920-931.

Chipman, L., Podgorski, D., Green, S., Kostka, J., Cooper, W., and Huettel, M. (2010) Decomposition of plankton-derived dissolved organic matter in permeable coastal sediments. Limnol Oceanogr 55: 857-871.

Cho, K.H., Hong, S.G., Cho, H.H., Lee, Y.K., Chun, J., and Lee, H.K. (2008) Maribacter arcticus sp. nov., isolated from Arctic marine sediment. Int J Syst Evol Microbiol 58:

1300-1303.

Choi, A., Yang, S.J., and Cho, J.C. (2013) Lutibacter flavus sp nov., a marine bacterium isolated from a tidal flat sediment. Int J Syst Evol Microbiol 63: 946-951.

Choi, D.H., and Cho, B.C. (2006) Lutibacter litoralis gen. nov., sp nov., a marine bacterium of the family Flavobacteriaceaeisolated from tidal flat sediment. Int J Syst Evol Microbiol 56: 771-776.

Choi, D.H., Hwang, C.Y., and Cho, B.C. (2009) Pelagibius litoralis gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceaeisolated from coastal seawater. Int J Syst Evol Microbiol 59: 818-823.

References

174

Coyte, K.Z., Tabuteau, H., Gaffney, E.A., Foster, K.R., and Durham, W.M. (2017) Microbial competition in porous environments can select against rapid biofilm growth. Proc Natl Acad Sci USA 114: E161-E170.

Cypionka, H. (2000) Oxygen respiration by Desulfovibrio species. Annu Rev Microbiol 54:

827-848.

D'Onofrio, A., Crawford, J.M., Stewart, E.J., Witt, K., Gavrish, E., Epstein, S. et al. (2010) Siderophores from neighboring organisms promote the growth of uncultured Bacteria.

Chem Biol 17: 254-264.

Daims, H., Lebedeva, E.V., Pjevac, P., Han, P., Herbold, C., Albertsen, M. et al. (2015) Complete nitrification by Nitrospirabacteria. Nature 528: 504-509.

Dale, N.G. (1974) Bacteria in intertidal sediments: factors related to their distribution. Limnol Oceanogr 19: 509-518.

Davis, K.E.R., Joseph, S.J., and Janssen, P.H. (2005) Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl Environ Microbiol 71: 826-834.

De Beer, D., and Stoodley, P. (2006) Microbial Biofilms. In The Prokaryotes: Volume 1:

Symbiotic associations, Biotechnology, Applied Microbiology. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., and Stackebrandt, E. (eds). New York, NY: Springer New York, pp. 904-937.

de Beer, D., Wenzhöfer, F., Ferdelman, T.G., Boehme, S.E., Huettel, M., van Beusekom, J.E.E. et al. (2005) Transport and mineralization rates in North Sea sandy intertidal sediments, Sylt-Rømø Basin, Wadden Sea. Limnol Oceanogr 50: 113-127.

de Castro Araújo, S., and Garcia, V.M.T. (2005) Growth and biochemical composition of the diatom Chaetoceros cf. wighamii brightwell under different temperature, salinity and carbon dioxide levels. I. Protein, carbohydrates and lipids. Aquaculture 246: 405-412.

de Haas, H., van Weering, T.C.E., and de Stieger, H. (2002) Organic carbon in shelf seas:

sinks or sources, processes and products. Continent Shelf Res 22: 691-717.

Delmont, T.O., Quince, C., Shaiber, A., Esen, Ö.C., Lee, S.T.M., Lücker, S., and Eren, A.M.

(2017) Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant In the surface ocean. bioRxiv: doi: https://doi.org/10.1101/129791

Delong, E.F., Franks, D.G., and Alldredge, A.L. (1993) Phylogenetic diversity of aggregate-attached vs free-living marine bacterial assemblages. Limnol Oceanogr 38: 924-934.

Dilling, W., and Cypionka, H. (1990) Aerobic respiration in sulfate-reducing bacteria. FEMS Microbiol Lett 71: 123-127.

Dombrowski, N., Seitz, K.W., Teske, A.P., and Baker, B.J. (2014) New insights into microbial hydrocarbon cycling and metabolic interdependencies in hydrothermal sediments. Microbiome: in press.

Dyksma, S., Bischof, K., Fuchs, B.M., Hoffmann, K., Meier, D., Meyerdierks, A. et al. (2016) Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments.

ISME J 10: 1939-1953.

Edgcomb, V.P., Pachiadaki, M.G., Mara, P., Kormas, K.A., Leadbetter, E.R., and Bernhard, J.M. (2016) Gene expression profiling of microbial activities and interactions in sediments under haloclines of E. Mediterranean deep hypersaline anoxic basins. ISME J 10: 2643-2657.

References

Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G. et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science 323: 133-138.

Eilers, H., Pernthaler, J., Glöckner, F.O., and Amann, R. (2000) Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl Environ Microbiol 66: 3044-3051.

Emery, K. (1968) Relict sediments on continental shelves of world. AAPG Bulletin 52.

Erbilgin, O., McDonald, K.L., and Kerfeld, C.A. (2014) Characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides. Appl Environ Microbiol 80: 2193-2205.

Fenchel, T. (2008) The microbial loop-25 years later. J Exp Mar Biol Ecol 366: 99-103.

Fernández-Gómez, B., Richter, M., Schüler, M., Pinhassi, J., Acinas, S.G., González, J.M., and Pedrós-Alio, C. (2013) Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J 7: 1026-1037.

Field, C.B., Behrenfeld, M.J., Randerson, J.T., and Falkowski, P. (1998) Primary production of the biosphere: Integrating terrestrial and oceanic components. Science 281: 237-240.

Flood, B.E., Jones, D.S., and Bailey, J.V. (2015) Sedimenticola thiotaurini sp nov., a sulfur-oxidizing bacterium isolated from salt marsh sediments, and emended descriptions of the genus Sedimenticola and Sedimenticola selenatireducens. Int J Syst Evol Microbiol 65:

2522-2530.

Franco, M.D., Vanaverbeke, J., Van Oevelen, D., Soetaert, K., Costa, M.J., Vincx, M., and Moens, T. (2010) Respiration partitioning in contrasting subtidal sediments: seasonality and response to a spring phytoplankton deposition. Mar Ecol-Evol Persp 31: 276-290.

Freitas, S., Hatosy, S., Fuhrman, J.A., Huse, S.M., Welch, D.B.M., Sogin, M.L., and Martiny, A.C. (2012) Global distribution and diversity of marine Verrucomicrobia. ISME J 6: 1499-1505.

Fuerst, J.A., and Sagulenko, E. (2011) Beyond the bacterium: Planctomycetes challenge our concepts of microbial structure and function. Nat Rev Micro 9: 403-413.

Gangi, A.F. (1985) Permeability of unconsolidated sands and porous rocks. J Geophys Res-Solid 90: 3099-3104.

Gattuso, J.P., Frankignoulle, M., and Wollast, R. (1998) Carbon and carbonate metabolism in coastal aquatic ecosystems. Annu Rev Ecol Syst 29: 405-434.

Gibbons, S.M., Caporaso, J.G., Pirrung, M., Field, D., Knight, R., and Gilbert, J.A. (2013) Evidence for a persistent microbial seed bank throughout the global ocean. Proc Natl Acad Sci USA 110: 4651-4655.

Gifford, S.M., Sharma, S., and Moran, M.A. (2014) Linking activity and function to ecosystem dynamics in a coastal bacterioplankton community. Front Microbiol 5:

doi:10.3389/fmicb.2014.00185.

Gihring, T.M., Humphrys, M., Mills, H.J., Huettel, M., and Kostka, J.E. (2009) Identification of phytodetritus-degrading microbial communities in sublittoral Gulf of Mexico sands.

Limnol Oceanogr 54: 1073-1083.

Gilbert, J.A., Field, D., Swift, P., Newbold, L., Oliver, A., Smyth, T. et al. (2009) The seasonal structure of microbial communities in the Western English Channel. Environ Microbiol 11: 3132-3139.

Giovannoni, S.J., Britschgi, T.B., Moyer, C.L., and Field, K.G. (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345: 60-63.

References

176

Giovannoni, S.J., Tripp, H.J., Givan, S., Podar, M., Vergin, K.L., Baptista, D. et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 1242-1245.

Gittel, A., Mussmann, M., Sass, H., Cypionka, H., and Könneke, M. (2008) Identity and abundance of active sulfate-reducing bacteria in deep tidal flat sediments determined by directed cultivation and CARD-FISH analysis. Environ Microbiol 10: 2645-2658.

Glöckner, F.O., Kube, M., Bauer, M., Teeling, H., Lombardot, T., Ludwig, W. et al. (2003) Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. Proc Natl Acad Sci USA 100: 8298-8303.

Gobet, A., Boetius, A., and Ramette, A. (2014) Ecological coherence of diversity patterns derived from classical fingerprinting and next generation sequencing techniques. Environ Microbiol 16: 2672-2681.

Gobet, A., Böer, S.I., Huse, S.M., van Beusekom, J.E.E., Quince, C., Sogin, M.L. et al. (2012) Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME J 6: 542-553.

Gómez-Pereira, P.R., Fuchs, B.M., Alonso, C., Oliver, M.J., van Beusekom, J.E.E., and Amann, R. (2010) Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean. ISME J 4: 472-487.

Gómez-Pereira, P.R., Schuler, M., Fuchs, B.M., Bennke, C., Teeling, H., Waldmann, J. et al.

(2012) Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean. Environ Microbiol 14: 52-66.

Gooday, A.J. (2002) Biological responses to seasonally varying fluxes of organic matter to the ocean floor: A review. J Oceanogr 58: 305-332.

Goodwin, S., McPherson, J.D., and McCombie, W.R. (2016) Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics 17: 333-351.

Hahnke, R.L., Bennke, C.M., Fuchs, B.M., Mann, A.J., Rhiel, E., Teeling, H. et al. (2015) Dilution cultivation of marine heterotrophic bacteria abundant after a spring phytoplankton bloom in the North Sea. Environ Microbiol 17: 3515-3526.

Hameed, A., Shahina, M., Lin, S.Y., Lai, W.A., Hsu, Y.-H., Liu, Y.C., and Young, C.C.

(2014) Aquibacter zeaxanthinifaciens gen. nov., sp nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from surface seawater, and emended descriptions of the genera Aestuariibaculum and Gaetbulibacter. Int J Syst Evol Microbiol 64: 138-145.

Haroon, M.F., Skennerton, C.T., Steen, J.A., Lachner, N., Hugenholtz, P., and Tyson, G.W.

(2013) In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery. Methods Enzymol 531: 3-19.

Harper, M.A. (1969) Movement and migration of diatoms on sand grains. British Phycological Journal 4: 97-103.

Hastings, D., and Emerson, S. (1988) Sulfate reduction in the presence of low oxygen levels in the water column of the Cariaco Trench. Limnol Oceanogr 33: 391-396.

Haug, A., and Myklestad, S. (1976) Polysaccharides of marine Diatomswith special reference to Chaetocerosspecies. Mar Biol 34: 217-222.

Haynes, K., Hofmann, T.A., Smith, C.J., Ball, A.S., Underwood, G.J.C., and Osborn, A.M.

(2007) Diatom-derived carbohydrates as factors affecting bacterial community composition in estuarine sediments. Appl Environ Microbiol 73: 6112-6124.

References

Hehemann, J.H., Kelly, A.G., Pudlo, N.A., Martens, E.C., and Boraston, A.B. (2012) Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. Proc Natl Acad Sci USA 109: 19786-19791.

Hemsworth, G.R., Dejean, G., Davies, G.J., and Brumer, H. (2016) Learning from microbial strategies for polysaccharide degradation. Biochem Soc T 44: 94-108.

Hirsch, P., and Müller, M. (1985) Planctomyces limnophilus sp. nov., a stalked and budding bacterium from freshwater. Syst Appl Microbiol 6: 276-280.

Hoagland, K.D., Rosowski, J.R., Gretz, M.R., and Roemer, S.C. (1993) Diatom extracellular polymeric substances: function, fine-structure, chemistry, and physiology. J Phycol 29:

537-566.

Horner-Devine, M.C., Leibold, M.A., Smith, V.H., and Bohannan, B.J.M. (2003) Bacterial diversity patterns along a gradient of primary productivity. Ecol Lett 6: 613-622.

Howarth, M.J., Dyer, K.R., Joint, I.R., Hydes, D.J., Purdie, D.A., Edmunds, H. et al. (1994) Seasonal cycles and their spatial variability. In Understanding the North Sea System.

Charnock, H., Dyer, K.R., Huthnance, J.M., Liss, P.S., Simpson, J.H., and Tett, P.B. (eds):

Springer Science and Business Media pp. 5-26.

Huettel, M., and Rusch, A. (2000) Transport and degradation of phytoplankton in permeable sediment. Limnol Oceanogr 45: 534-549.

Huettel, M., Ziebis, W., and Forster, S. (1996) Flow-induced uptake of particulate matter in permeable sediments. Limnol Oceanogr 41: 309-322.

Huettel, M., Berg, P., and Kostka, J.E. (2014) Benthic exchange and biogeochemical cycling in permeable sediments. In Annual Review of Marine Science. Carlson, C.A., and Giovannoni, S.J. (eds). Palo Alto: Annual Reviews, pp. 23-51.

Hugenholtz, P., Goebel, B.M., and Pace, N.R. (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180: 4765-4774.

Hunter, E.M., Mills, H.J., and Kostka, J.E. (2006) Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments. Appl Environ Microbiol 72: 5689-5701.

Huse, S.M., Dethlefsen, L., Huber, J.A., Welch, D.M., Relman, D.A., and Sogin, M.L. (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PloS Genet 4: e1000255.

Izumi, H., Sagulenko, E., Webb, R.I., and Fuerst, J.A. (2013) Isolation and diversity of Planctomycetes from the sponge Niphates sp., seawater, and sediment of Moreton Bay, Australia. Anton Leeuw Int J G 104: 533-546.

Jago, C.F., Jones, S.E., Latter, R.J., McCandliss, R.R., Hearn, M.R., and Howarth, M.J.

(2002) Resuspension of benthic fluff by tidal currents in deep stratified waters, northern North Sea. J Sea Res 48: 259-269.

Jahnke, R. (1985) A model of microenvironments in deep-sea sediments: formation and effects on porewater profiles. Limnol Oceanogr 30: 956-965.

Jahnke, R., Richards, M., Nelson, J., Robertson, C., Rao, A., and Jahnke, D. (2005) Organic matter remineralization and porewater exchange rates in permeable South Atlantic Bight continental shelf sediments. Cont Shelf Res 25: 1433-1452.

References

178

Jahnke, R.A. (2010) Global Synthesis. In Carbon and Nutrient Fluxes in Continental Margins: A Global Synthesis. Liu, K.-K., Atkinson, L., Quiñones, R., and Talaue-McManus, L. (eds). Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 597-615.

Jahnke, R.A., Nelson, J.R., Marinelli, R.L., and Eckman, J.E. (2000) Benthic flux of biogenic elements on the southeastern US continental shelf: influence of pore water advective transport and benthic microalgae. Continent Shelf Res 20: 109-127.

Jeske, O., Jogler, M., Petersen, J., Sikorski, J., and Jogler, C. (2013) From genome mining to phenotypic microarrays: Planctomycetes as source for novel bioactive molecules. Antonie Van Leeuwenhoek 104: 551-567.

Jeske, O., Schüler, M., Schumann, P., Schneider, A., Boedeker, C., Jogler, M. et al. (2015) Planctomycetes do possess a peptidoglycan cell wall. Nat Commun 6.

Joiris, C., Billen, G., Lancelot, C., Daro, M.H., Mommaerts, J.P., Bertels, A. et al. (1982) A budget of carbon cycling in the Belgian coastal zone: relative roles of zooplankton, bacterioplankton and benthos in the utilization of primary production. Netherlands Journal of Sea Research 16: 260-275.

Jongkees, S.A.K., and Withers, S.G. (2014) Unusual enzymatic glycoside cleavage mechanisms. Accounts Chem Res 47: 226-235.

Jørgensen, B.B. (1977) The sulfur cycle of a coastal marine sediment (Limfjorden, Denmark).

Limnol Oceanogr 22: 814-832.

Jørgensen, B.B. (2006) Bacteria and marine biogeochemistry. In Marine Geochemistry.

Schulz, H.D., and Zabel, M. (eds). Berlin, Heidelberg: Springer Berlin Heidelberg, pp.

169-206.

Jørgensen, B.B., and Boetius, A. (2007) Feast and famine - microbial life in the deep-sea bed.

Nat Rev Microbiol 5: 770-781.

Jørgensen, B.B., Bang, M., and Blackburn, T.H. (1990) Anaerobic mineralization in marine sediments from the Baltic-Sea-North Sea transition. Mar Ecol Prog Ser 59: 39-54.

Julies, E.M., Fuchs, B.M., Arnosti, C., and Brüchert, V. (2010) Organic carbon degradation in anoxic organic-rich shelf sediments: Biogeochemical rates and microbial abundance.

Geomicrobiol J 27: 303-314.

Jung, Y.T., Lee, J.S., and Yoon, J.H. (2014) Maribacter caenipelagi sp. nov., a member of the Flavobacteriaceae isolated from a tidal flat sediment of the Yellow Sea in Korea. Anton Leeuw Int J G 106: 733-742.

Kabisch, A., Otto, A., Konig, S., Becher, D., Albrecht, D., Schuler, M. et al. (2014) Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes 'Gramella forsetii' KT0803. ISME J 8: 1492-1502.

Kanukollu, S., Wemheuer, B., Herber, J., Billerbeck, S., Lucas, J., Daniel, R. et al. (2016) Distinct compositions of free-living, particle-associated and benthic communities of the Roseobactergroup in the North Sea. FEMS Microbiol Ecol 92: fiv145.

Kenne, L., and Lindberg, B. (1983) Bacterial polysaccharides In The Polysaccharides.

Aspinall, G.O. (ed). New York, New York: Academic Press, Inc., pp. 287-363.

Kim, J.W., Brawley, S.H., Prochnik, S., Chovatia, M., Grimwood, J., Jenkins, J. et al. (2016a) Genome analysis of Planctomycetesinhabiting blades of the red alga Porphyra umbilicalis.

PloS One 11: e0151883.