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Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria.

ABSTRACT: Biofilms can provide a number of different ecological niches for microorganisms. Here, a multispecies biofilm was studied in which pyrite-oxidizing microbes are the primary producers. Its stability allowed not only detailed fluorescence in situ hybridization (FISH)-based characterization of the microbial population in different areas of the biofilm but also to integrate these results with oxygen and pH microsensor measurements conducted before. The O2 concentration declined rapidly from the outside to the inside of the biofilm. Hence, part of the population lives under microoxic or anoxic conditions. Leptospirillum ferrooxidans strains dominate the microbial population but are only located in the oxic periphery of the snottite structure. Interestingly, archaea were identified only in the anoxic parts of the biofilm. The archaeal community consists mainly of so far uncultured Thermoplasmatales as well as novel ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganism) species. Inductively coupled plasma analysis and X-ray absorption near edge structure spectra provide further insight in the biofilm characteristics but revealed no other major factors than oxygen affecting the distribution of bacteria and archaea. In addition to catalyzed reporter deposition FISH and oxygen microsensor measurements, microautoradiographic FISH was used to identify areas in which active CO2 fixation takes place. Leptospirilla as well as acidithiobacilli were identified as primary producers. Fixation of gaseous CO2 seems to proceed only in the outer rim of the snottite. Archaea inhabiting the snottite core do not seem to contribute to the primary production. This work gives insight in the ecological niches of acidophilic microorganisms and their role in a consortium. The data provided the basis for the enrichment of uncultured archaea.

SUBMITTER: Ziegler S

PROVIDER: S-EPMC3749503 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature

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Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria.

Ziegler Sibylle S Dolch Kerstin K Geiger Katharina K Krause Susanne S Asskamp Maximilian M Eusterhues Karin K Kriews Michael M Wilhelms-Dick Dorothee D Goettlicher Joerg J Majzlan Juraj J Gescher Johannes J

The ISME journal 20130425 9

Biofilms can provide a number of different ecological niches for microorganisms. Here, a multispecies biofilm was studied in which pyrite-oxidizing microbes are the primary producers. Its stability allowed not only detailed fluorescence in situ hybridization (FISH)-based characterization of the microbial population in different areas of the biofilm but also to integrate these results with oxygen and pH microsensor measurements conducted before. The O2 concentration declined rapidly from the outs ...[more]

PMID: 23619304

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Project description:The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNACys is first acylated with phosphoserine (Sep) by O-phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNACys by Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota, TACK, and Asgard) and two groups of bacteria ("Candidatus Parcubacteria" and Chloroflexi). Bacterial SepRS and SepCysS charged bacterial tRNACys species with cysteine in vitro Homologs of SepCysE, a scaffold protein facilitating SepRS⋅SepCysS complex assembly in Euryarchaeota class I methanogens, are found in a few groups of TACK and Asgard archaea, whereas the C-terminally truncated homologs exist fused or genetically coupled with diverse SepCysS species. Investigation of the selenocysteine (Sec)- and pyrrolysine (Pyl)-utilizing traits in SepRS-utilizing archaea and bacteria revealed that the archaea carrying full-length SepCysE employ Sec and that SepRS is often found in Pyl-utilizing archaea and Chloroflexi bacteria. We discuss possible contributions of the SepRS-SepCysS system for sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes.IMPORTANCE Comprehensive analyses of all genomic and metagenomic protein sequence data in public databases revealed the distribution and evolution of an alternative cysteine-encoding system in diverse archaea and bacteria. The finding that the SepRS-SepCysS-SepCysE- and the selenocysteine-encoding systems are shared by the Euryarchaeota class I methanogens, the Crenarchaeota AK8/W8A-19 group, and an Asgard archaeon suggests that ancient archaea may have used both systems. In contrast, bacteria may have obtained the SepRS-SepCysS system from archaea. The SepRS-SepCysS system sometimes coexists with a pyrrolysine-encoding system in both archaea and bacteria. Our results provide additional bioinformatic evidence for the contribution of the SepRS-SepCysS system for sulfur assimilation and diverse metabolisms which require vast amounts of iron-sulfur enzymes and proteins. Among these biological activities, methanogenesis, methylamine metabolism, and organohalide respiration may have local and global effects on earth. Taken together, uncultured bacteria and archaea provide an expanded record of the evolution of the genetic code.

Project description:Various strategies to accelerate the formation of biofilms on minerals have been studied, and one of them is the use of D-galactose as an inducer of EPS production in planktonic cells of biooxidant bacteria. With the aim to evaluate the influence on the attachment and the effect over the solubilization of a polymetallic mineral concentrate, the behavior of a microbial consortium formed by Acidithiobacillus thiooxidans DSM 14887T and Leptospirillum ferrooxidans DSM 2705T previously induced with D-galactose for the early formation of EPS was studied. These microorganisms were previously adapted to 0.15 and 0.25% of D-galactose, respectively; afterward, different proportions of both strains were put in contact with the particle surface of a concentrate of polymetallic mineral. Also, to evaluate the affinity of each bacterium to the mineral, attachment tests were carried out with one of these species acting as a pre-colonizer. The same consortia were used to evaluate the solubilization of the polymetallic mineral. The results obtained show that the induction by D-galactose increases the microbial attachment percentage to the mineral by at least 10% with respect to the control of non-adapted consortia. On the other hand, the tests carried out with pre-colonization show that the order of inoculation also affects the microbial attachment percentage. From the different proportions tested, it was determined that the use of a consortium with a proportion of 50% of each species previously adapted to D-galactose and inoculated simultaneously, present a microbial attachment percentage to the mineral greater than 95% and better solubilization of a polymetallic mineral, reaching values of 9.7 and 11.7mgL-1 h-1 of Fe3+ and SO4 2-, respectively. Therefore, the use of D-galactose in small concentrations as inducer of EPS in acidophilic cells and the selection of an adequate strategy of inoculation can be beneficial to improve biooxidation since it would allow this process to develop in a shorter time by achieving a greater number of attached cells in a shorter time accelerating the solubilization of a sulfide mineral. Graphical AbstractEPS production using D-galactose as inducer and its influence in the attachment of consortia formed by differents proportions of A. thiooxidans and L. ferrooxidans inoculated at the same time and when one of them acting as a pre-colonizer.

Dataset Information

Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria.

Publications

Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria.

Similar Datasets

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