Distribution of Dehalococcoidia in marine sediments and strategies for their enrichment

The marine subsurface is one of the largest microbial habitats on Earth. Microbial community studies based on the 16S rRNA gene have revealed that bacteria of the class Dehalococcoidia, phylum Chloroflexi, are one of the most widespread and abundant bacteria inhabiting the marine subsurface. However, their physiology and ecological role are unknown. In this study, marine sediments were cultivated with various potential electron acceptors to explore respiration modes catalysed by Dehalococcoidia. The cultivation revealed that Dehalococcoidia can be cultivated in an anoxic minimal medium amended with hydrogen and acetate as potential electron donor and carbon source, respectively, at a temperature of 30ºC and at atmospheric pressure, and thus Dehalococcoidia are not strict piezophilic bacteria. An increase in Dehalococcoidia 16S rRNA gene copy numbers of one order of magnitude, as evidenced by quantitative PCR with newly designed primers, could be observed in a time span of months for several sediment cultures, indicating that their replication times are not in geological times, i.e., thousands to millions of years. Dehalococcoidia 16S rRNA gene copy numbers (in the range of 10^2–10^5 ml^-1 culture) among the various sediment cultures inoculated with diverse sediments and amended with different potential electron acceptors suggested no specific respiratory mode to be preferred by subseafloor Dehalococcoidia. Additionally, subseafloor Dehalococcoidia were not reliant on organohalide respiration under the conditions tested, in contrast to cultivated Dehalococcoidia species such as Dehalococcoides mccartyi. Interestingly, among the tested organohalide compounds, 1,2,3-trichlorobenzene was transformed to 1,3-dichlorobenzene in sediment cultures. Inhibition studies using antibiotics against Gram-positives and microbial community analyses by 454-pyrosequencing of 16S rRNA genes, indicated members affiliated with the phylum Firmicutes were involved in the transformation of 1,2,3-trichlorobenzene. The presence, abundance, and distribution of Dehalococcoidia were investigated in sediments of the Arctic Baffin Bay. Geochemical studies showed the shelf as an area rich in organic matter, with indications for the presence of sulphate reduction (highest dsrA gene copies and a decrease in sulphate concentration in its pore-waters). On the other hand, the basin area was comparably poor in organic matter with high concentrations of iron(II) and manganese(II) in its pore-waters. Dehalococcoidia were present at all investigated sites and depths in the range of 1.1 x 10^3–8.4 x 10^5 16S rRNA gene copy numbers g^-1 sediment. Dehalococcoidia copy numbers were highest and generally stable with depth in shelf sites of the Baffin Bay compared to any other area. In contrast, Dehalococcoidia copy numbers pronouncedly decreased with depth at basin sites. Dehalococcoidia accounted for the highest proportion of the total bacterial 16S rRNA genes when low bacterial copy numbers were found, mostly in samples from deeper sediment layers, indicating that subseafloor Dehalococcoidia are resilient to burial. Illumina sequencing of 16S rRNA genes gave further evidence that Dehalococcoidia were mostly associated with shelf sediments. The relative abundance of Dehalococcoidia and, most specifically, the clade GIF-9 within the class Dehalococcoidia, positively correlated with organic matter content, and negatively correlated with sulphate and manganese(II) pore-water concentrations. Thus, a potential fermenting metabolism is likely for GIF-9 members. Apart from Dehalococcoidia, the Baffin Bay bacterial community was dominated by members of the class Betaproteobacteria (with relative abundance of 38 to 64%), and specifically the order Burkholderiales, which strongly correlated to manganese(II) pore-water concentration, suggesting a metal respiratory metabolism. In contrast to Dehalococcoidia, the class Betaproteobacteria is not commonly found as widely distributed and abundant bacterial group in the marine subseafloor, and its presence and high abundance in sediments of the Baffin Bay may be the result of the glacial conditions in the area.

Author dc:creator

• Algora, Camelia

Advisor dc:contributor.advisor

• Adrian, Lorenz

Licence dc:rights.uri

• https://creativecommons.org/licenses/by-nc-nd/4.0/

Language dc:language.iso

en

Identifier URI

http://dx.doi.org/10.14279/depositonce-5587

OAI identifier oai:identifier

oai:depositonce.tu-berlin.de:11303/6000