Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov.

Holmes, Dawn E.; Nevin, Kelly P.; Lovley, Derek R.

doi:10.1099/ijs.0.02958-0

Cited by 151 publications

(132 citation statements)

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“…Alignments of translated nucleotide sequences and Neighbour-Joining phylogenetic trees were generated in Geneious Pro 5.6 (www.geneious.com, accessed 14 December 2014) [44] [45] served to correct for possible variations in DNA extraction efficiencies Table 1. List of primers used in the current study with respective primer sequence, and details for the PCR, qPCR and clone library approaches A/2, C/2, D/1 and D/3 dmdA primers are from Varaljay et al [42] ; recA primers from Holmes et al [46] Position numbers for dmdA gene refer to the full-length dmdA sequence of Ruegeria pomeroyi DSS-3 [42] Primer name Table 1) amplify a 212 bp region of the bacterial recA gene. [46] Each 10 mL reaction consisted of 1Â LightCycler 480 SYBR Green I Mastermix (containing FastStart taq polymerase, reaction buffer, dNTP's, SYBR Green I dye and MgCl 2 ; Roche), 1 mM of each primer (see Table 1 for respective primers), and 3 mL of template DNA.…”

Section: Determination Of Dmsp and Symbiodinium Abundances In Coral Tmentioning

confidence: 99%

Dimethylsulfoniopropionate in corals and its interrelations with bacterial assemblages in coral surface mucus

Frade¹,

Schwaninger²,

Glasl³

et al. 2016

Environ. Chem.

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Environmental context. Corals produce copious amounts of dimethylsulfoniopropionate (DMSP), a sulfur compound implicated in climate regulation. We studied DMSP concentrations inside corals and unveiled the linkage between DMSP availability and the abundance of DMSP-degrading bacterial groups inhabiting the corals' surface. Our findings suggest that DMSP mediates the interplay between corals and microbes, highlighting the importance of sulfur compounds for microbial processes in corals and for the resilience of coral reef ecosystems.Abstract. Corals produce copious amounts of dimethylsulfoniopropionate (DMSP), a sulfur compound thought to play a role in structuring coral-associated bacterial communities. We tested the hypothesis that a linkage exists between DMSP availability in coral tissues and the community dynamics of bacteria in coral surface mucus. We determined DMSP concentrations in three coral species (Meandrina meandrites, Porites astreoides and Siderastrea siderea) at two sampling depths (5 and 25 m) and times of day (dawn and noon) at Curaçao, Southern Caribbean. DMSP concentration (4-409 nmol cm À2 coral surface) varied with host species-specific traits such as Symbiodinium cell abundance, but not with depth or time of sampling. Exposure of corals to air caused a doubling of their DMSP concentration. The phylogenetic affiliation of mucus-associated bacteria was examined by clone libraries targeting three main subclades of the bacterial DMSP demethylase gene (dmdA). dmdA gene abundance was determined by quantitative Polymerase Chain Reaction (qPCR) against a reference housekeeping gene (recA). Overall, a higher availability of DMSP corresponded to a lower relative abundance of the dmdA gene, but this pattern was not uniform across all host species or bacterial dmdA subclades, suggesting the existence of distinct DMSP microbial niches or varying dmdA DMSP affinities. This is the first study quantifying dmdA gene abundance in corals and linking related changes in the community dynamics of DMSP-degrading bacteria to DMSP availability. Our study suggests that DMSP mediates the regulation of microbes by the coral host and highlights the significance of sulfur compounds for microbial processes in coral reefs.

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Section: Determination Of Dmsp and Symbiodinium Abundances In Coral Tmentioning

confidence: 99%

Dimethylsulfoniopropionate in corals and its interrelations with bacterial assemblages in coral surface mucus

Frade¹,

Schwaninger²,

Glasl³

et al. 2016

Environ. Chem.

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“…Rf4 to the uncultured methanogenic archaeon RC-I. The recipient was isolated from the rice rhizosphere (Erkel et al 2006), while the donor belongs to the Geobacteraceae that resides both in soil and water and is probably capable of nitrogen fixation (Holmes et al 2004). We note, however, that the genome sample of archaebacterial species in the public databases is very limited.…”

Section: Community Structure In the Directed Network Of Recent Lgtmentioning

confidence: 99%

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

Popa

Hazkani‐Covo²,

Landan³

et al. 2011

Genome Res.

224

204

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Lateral gene transfer (LGT) plays a major role in prokaryote evolution with only a few genes that are resistant to it; yet the nature and magnitude of barriers to lateral transfer are still debated. Here, we implement directed networks to investigate donor-recipient events of recent lateral gene transfer among 657 sequenced prokaryote genomes. For 2,129,548 genes investigated, we detected 446,854 recent lateral gene transfer events through nucleotide pattern analysis. Among these, donor-recipient relationships could be specified through phylogenetic reconstruction for 7% of the pairs, yielding 32,028 polarized recent gene acquisition events, which constitute the edges of our directed networks. We find that the frequency of recent LGT is linearly correlated both with genome sequence similarity and with proteome similarity of donor-recipient pairs. Genome sequence similarity accounts for 25% of the variation in gene-transfer frequency, with proteome similarity adding only 1% to the variability explained. The range of donor-recipient GC content similarity within the network is extremely narrow, with 86% of the LGTs occurring between donor-recipient pairs having #5% difference in GC content. Hence, genome sequence similarity and GC content similarity are strong barriers to LGT in prokaryotes. But they are not insurmountable, as we detected 1530 recent transfers between distantly related genomes. The directed network revealed that recipient genomes of distant transfers encode proteins of nonhomologous end-joining (NHEJ; a DNA repair mechanism) far more frequently than the recipient lacking that mechanism. This implicates NHEJ in genes spread across distantly related prokaryotes through bypassing the donor-recipient sequence similarity barrier.

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“…This may not be surprising because in petroleum-contaminated aquifers and in aquifers amended with organic electron donors to promote dissimilatory metal reduction there is likely to be an abundance of organic carbon, but limiting quantities of other nutrients. Although Geobacter species can overcome limitations for fixed nitrogen by fixation of abundant nitrogen gas (Bazylinski et al, 2000;Coppi et al, 2001;Holmes et al, 2004a), phosphate sources are likely to be more limited. Until now it has not been possible to assess possible phosphate limitations of Geobacter species because of a lack of information on genes, which might be indicative of phosphate limitation.…”

Section: Introductionmentioning

confidence: 99%

Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer

et al. 2009

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Nutrient limitation is an environmental stress that may reduce the effectiveness of bioremediation strategies, especially when the contaminants are organic compounds or when organic compounds are added to promote microbial activities such as metal reduction. Genes indicative of phosphatelimitation were identified by microarray analysis of chemostat cultures of Geobacter sulfureducens. This analysis revealed that genes in the pst-pho operon, which is associated with a high-affinity phosphate uptake system in other microorganisms, had significantly higher transcript abundance under phosphate-limiting conditions, with the genes pstB and phoU upregulated the most. Quantitative PCR analysis of pstB and phoU transcript levels in G. sulfurreducens grown in chemostats demonstrated that the expression of these genes increased when phosphate was removed from the culture medium. Transcripts of pstB and phoU within the subsurface Geobacter species predominating during an in situ uranium-bioremediation field experiment were more abundant than in chemostat cultures of G. sulfurreducens that were not limited for phosphate. Addition of phosphate to incubations of subsurface sediments did not stimulate dissimilatory metal reduction. The added phosphate was rapidly adsorbed onto the sediments. The results demonstrate that Geobacter species can effectively reduce U(VI) even when experiencing suboptimal phosphate concentrations and that increasing phosphate availability with phosphate additions is difficult to achieve because of the high reactivity of this compound. This transcript-based approach developed for diagnosing phosphate limitation should be applicable to assessing the potential need for additional phosphate in other bioremediation processes.

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Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov.

Abstract: Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov.

Cited by 151 publications

References 50 publications

Dimethylsulfoniopropionate in corals and its interrelations with bacterial assemblages in coral surface mucus

Dimethylsulfoniopropionate in corals and its interrelations with bacterial assemblages in coral surface mucus

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer

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