Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters

Abstract

Intraterrestrial waters harbor microbial communities being extensively studied to understand microbial processes underlying subsurface ecosystem functioning. This paper provides the results of an investigation on the microbiomes of unique, subsurface sulfidic waters associated with Upper Jurassic, Cretaceous, and Miocene sediments. We used high-throughput 16S rDNA amplicon sequencing to reveal the structure of bacterial and archaeal communities in water samples differing in sulfide content (20–960 mg/dm 3 ), salinity (1.3–3.2%), and depth of extraction (60–660 m below ground level). Composition of the bacterial communities strongly varied across the samples; however, the bacteria participating in the sulfur cycle were common in all sulfidic waters. The shallowest borehole water (60 m bgl) was dominated by sulfur-oxidizing Epsilonproteobacteria ( Sulfurimonas , Sulfurovum ). In the waters collected from greater depths (148–300 m bgl), the prevalence of Betaproteobacteria ( Comamonadaceae ) and sulfate/sulfur-reducing Deltaproteobacteria ( Desulfopila , Desulfomicrobium , MSBL7 ) was observed. Sulfate reducers (members of Clostridia : Candidatus Desulforudis ) were the most abundant bacteria in the deepest borehole water (660 m bgl). Out of 850 bacterial OTUs, only one, affiliated with the Comamonadaceae family, was found abundant (> 1% of total bacterial sequences) in all samples. Contribution of Archaea to the whole microbial communities was lower than 0.5%. Archaeal communities did not differ across the samples and they consisted of Halobacteriaceae . Out of 372 archaeal OTUs, five, belonging to the four genera Natronomonas , Halorubrum , Halobellus , and Halorhabdus , were the most numerous. Electronic supplementary material The online version of this article (10.1007/s00248-018-1270-5) contains supplementary material, which is available to authorized users.

Microbial Communities of the Drinking Water With Gradient Radon Concentration Are Primarily Contributed by Radon and Heavy Metal Content

“…In Dotplot analysis, out of a total of 52 differentially abundant OTUs, the OTUs that were significantly enriched in contaminated sites are affiliated to the genera Candidatus Nitrotoga, unclassified Comamonadaceae, unclassified Parcubacteria, and the genera Rhizobium. Nitrite-oxidizing Candidatus Nitrotoga are widespread in a natural environment (Kitzinger et al, 2018), while unclassified Comamonadaceae is a dominant member of ancient subsurface and groundwater microbial communities in sulfidic waters reported as potential nitrate reducers and sulfur oxidizers (Deja-Sikora et al, 2019). The bacterial member of Parcubacteria has been reported as a dominant uncultivable microbe in a radiation-contaminated groundwater environment with limited metabolic genes, supporting their presence in contaminated sites which were considered in this investigation as a radiation-rich nutrientdeprived environment (Wrighton et al, 2012;Brown et al, 2015).…”

“…The bacterial assemblages mentioned above were found to be dominated in contaminated radon water and were reported to be abundantly inhabitant in radiation and chemolithotrophic environments (Poirel et al, 2008;Brown et al, 2015;Rao et al, 2016;Danczak et al, 2017), thus supporting our finding. On the other side, dominant families present in the control water were generally reported to be present in natural soil and drinking water (Li et al, 2016;Deja-Sikora et al, 2019). This difference in communities between the contaminated and control sites is supported by PERMANOVA (p 0.001) and Bray-Curtis dissimilarity cluster analysis that separates the control site from the cluster of contaminated sites.…”

“…Therefore, radiation and HM help in the enrichment of radiation-resistant, chemolithotrophic, and reactive oxygen hydrolytic enzyme-producing microbes so that they are sustained in contaminated sites over the inhabitant microbes from normal water. A few of the selected members of the microbial communities in the investigated sites from the family level, that is, Comamonadaceae, Rhodocyclaceae, and Pseudomonadaceae, unclassified Parcubacteria, Pseudorhodoferax, Sideroxydans, Nitrospira, unclassified Gammaproteobacteria, unclassified Betaproteobacteria, unclassified Methylocystaceae, unclassified Comamonadaceae, and Candidatus Methylomirabilis, are well reported to be abundant in radionuclide-and HMcontaminated environments, and they also pose a strong radionuclide-and HM-removing ability (Brown et al, 2015;Drewniak et al, 2016;Yan et al, 2016;Dahal et al, 2017;Kitzinger et al, 2018;Deja-Sikora et al, 2019); therefore, they can serve as a potential target for in situ bioremediation through bioaugmentation or biostimulation.…”

In situ modelling of biofilm formation in a hydrothermal spring cave

“…To our knowledge, this is the first report about such extraordinary high relative abundance of an OTU in the thermal waters of karst caves. Deja-Sikora et al 27 reported a similar phenomenon, the dominance of one unclassified Betaproteobacteria OTU affiliated with Comamonadaceae (abundance ranging from 1.7 to 57.8%) in sulfide-rich waters of the Carpathian Foredeep. The authors assumed that members of Comamonadaceae were likely to represent archetypal microbial species in those waters.…”

Sediment Microbial Fuel Cell Power Boosted by Natural Chitin Degradation and Oxygen Reduction Electrocatalysts

“…[48] Even the great diversity at genera level in the anode, most of them have been reported as electroactive bacteria. The great abundance of MSBL7, a sulfate/sulfur-reducing Deltaproteobacteria [49] in the anode biofilm is striking (Figure 6a,b); moreover, the high proportion of uncultured Deltaproteobacteria depicts the extraordinary bacterial www.advancedsciencenews.com www.clean-journal.com diversity not yet studied and cultured. In the anodic sediment, the abundant genera Desulfatiglans and Synthrophomonas have been described [50,51] as hydrocarbon degraders and synthrophic lifestyle (Figure 6b), [52,53] sulfate reducers and long chain fatty acid oxidizing bacteria.…”