Response of an Arctic Sediment Nitrogen Cycling Community to Increased CO2

Ocean acidification influences sediment/water nitrogen fluxes, possibly by impacting on the microbial process of ammonia oxidation. To investigate this further, undisturbed sediment cores collected from Ny Alesund harbour (Svalbard) were incubated with seawater adjusted to CO2 concentrations of 380, 540, 760, 1,120 and 3,000 μatm. DNA and RNA were extracted from the sediment surface after 14 days' exposure and the abundance of bacterial and archaeal ammonia oxidising (amoA) genes and transcripts quantified using quantitative polymerase chain reaction. While there was no change to the abundance of bacterial amoA genes, an increase to 760 μatm pCO2 reduced the abundance of bacterial amoA transcripts by 65 %, and this was accompanied by a shift in the composition of the active community. In contrast, archaeal amoA gene and transcript abundance both doubled at 3,000 μatm, with an increase in species richness also apparent. This suggests that ammonia oxidising bacteria and archaea in marine sediments have different pH optima, and the impact of elevated CO2 on N cycling may be dependent on the relative abundances of these two major microbial groups. Further evidence of a shift in the balance of key N cycling groups was also evident: the abundance of nirS-type denitrifier transcripts decreased alongside bacterial amoA transcripts, indicating that NO3 − produced by bacterial nitrification fuelled denitrification. An increase in the abundance of Planctomycete-specific 16S rRNA, the vastmajority of which grouped with known anammox bacteria, was also apparent at 3,000 μatm pCO2. This could indicate a possible shift from coupled nitrification–denitrification to anammox activity at elevated CO2.

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.

Evolution of the Diatoms: VIII. Re-Examination of the SSU-Rrna Gene Using Multiple Outgroups and a Cladistic Analysis of Valve Features.

The resolution of the SSU rRNA gene for phylogenetic analysis in the diatoms has been evaluated by Theriot et al. who claimed that the SSU rRNA gene could not be used to resolve the monophyly of the three diatoms classes described by Medlin and Kaczmarska. Although they used both only bolidomonads and heterokonts as outgroups, they did not explore outgroups further away than the heterokonts. In this study, the use of the multiple outgroups inside and outside the heterokonts with the rRNA gene for recovering the three monophyletic clades at the class level is evaluated. Trees with multiple outgroups ranging from only bolidophytes to Bacteria and Archea were analyzed with Bayesian and Maximum Likelihood analyses and two data sets were recovered with the classes being monophyletic. Other data sets were analyzed with non-weighted and weighted maximum parsimony. The latter reduced the number of clades and lengthened branch lengths between the clades. One data set using a weighted analysis recovered the three classes as monophyletic. Taking only bolidophytes as the only outgroup never produced monophyletic clades. Multiple outgroups including many heterokonts and certain members of the crown group radiation recovered monophyletic clades. The three classes can be defined by clear morphological differences primarily based on auxospore ontogeny and envelope structure, the presence or absence of a structure (tube process or sternum) associated with the annulus and the location of the cribrum in those genera with loculate areolae. A cladistic analysis of some of these features is presented and recovers the three classes.