While the key role of the bacterioplankton in OM cycling is well-studied (Azam et al., 1983; Rinta-Kanto et al., 2012; Beier et al., 2014; Buchan et al., 2014; Teeling et al., 2016), relatively little is known about the functional involvement of benthic microorganisms in OM cycling. During spring phytoplankton blooms the bacterioplankton community composition is dynamic, which allows studying shifts in the functional responses of communities by metagenomic analysis (Teeling et al., 2012; Teeling et al., 2016). The benthic community also reacts to phytoplankton blooms (Ruff et al., 2014; Mohit et al., 2015; Tait et al., 2015).
However, despite a seasonally changing activity, its’ community composition is much more stable and diverse than for the bacterioplankton (Böer et al., 2009; Gobet et al., 2012).
Consequently, we sequenced total RNA to reduce the functional and sequence diversity and to target transcribed genes only (Chapter III). The analysis presents ongoing research and is yet preliminary. At the time point of writing this thesis, a comprehensive assessment of prevalent functions, spatiotemporal dynamics and functional roles of microbial clades would be premature.
Despite the high proportion of transcripts related to photosynthesis (36% to 53%) and transcription and translation (6% to 10%, Chapter III), this data set is valuable. Dominance of photosynthesis- and housekeeping-related transcripts are intrinsic to metatranscriptomic datasets (Poretsky et al., 2005; Gifford et al., 2014; Thureborn et al., 2016). Nevertheless, with 4.5 × 106 (March_1) to 7.2 × 106 (May_deep3) mRNA reads (not considering April_1 enriched in eukaryotic RNA) for each sampling condition (date/depth), numbers of reads available for analysis are in the upper range compared to 5 × 103 to 5.7 × 107 for previously
General Conclusion and Outlook
166
published datasets (Urich et al., 2014; Edgcomb et al., 2016; Militon et al., 2016; Thureborn et al., 2016). Consequently, the following future work is suggested:
Metatranscriptome assembly
Low annotation rate of short read data (average 233 nt or translated 78 AA) was a shortcoming of this thesis. For example, median amino acid (AA) length of hidden Markov models (of 144 GH families) used for annotation of glycoside hydrolases is 282 AA.
Successful annotation of transcripts as GH required the mRNA transcript to cover at least 30% of the HMM (93 AA). Consequently, most GH could not be detected. Future work shall implement a de novo metatranscriptome assembly. Initial assembly tests resulted in transcript lengths with a N50 value of 308 nt (102 AA), enabling much higher sensitivity for functional annotation.
Organism-centric mapping of transcripts to reference database
In contrast to a function-centric approach, the organism-centric approach reveals the actual metabolic pathways intrinsic to a distinct population (McMahon, 2015). As outlined in this general discussion, members of the Planctomycetes are a clade of prime importance. Due to the high sequence complexity of the short read metatranscriptome, an organism-centric analysis of the transcripts requires the mapping of transcripts onto a reference genomic dataset (Rinta-Kanto et al., 2012; Wemheuer et al., 2015; Delmont et al., 2017). As community compositions of Planctomycetes are largely identical between pelagic and benthic habitats (Chapter I), publically available genomic data of Planctomycetes from other habitats than sediments can serve as a reference (compiled in Supplementary Table S1). However, mapping of transcripts should preferentially be performed with genomes from identical sediment sites (Carvalhais et al., 2012). Consequently, the Planctomycetes genomic reference data set should be obtained from site HelRoads using targeted metagenomics. Mapping of the metatranscriptome onto the reference genomic data will then result in a partial transcriptomic dataset of Planctomycetes under in situ conditions. This will help to reveal the Planctomycetes niche on the benthic communities’ metabolic map, giving deep insights into the autecology of this highly abundant taxon in sandy subtidal sediments.
General Conclusion and Outlook: Appendix
Appendix
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)
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