luxSin bacteria isolated from 25- to 40-million-year-old amber

Abstract

Interspecies bacterial communication is mediated by autoinducer-2, whose synthesis depends on luxS. Due to the apparent universality of luxS (present in over 40 bacterial species), it may have an ancient origin; however, no direct evidence is currently available. We amplified luxS in bacteria isolated from 25 to 40 million year-old amber. Phylogenies and Principal Component Analyses (PCA) of luxS and the 16S rRNA gene from ancient and extant bacteria were constructed. Amber isolates exhibited unique 16S rRNA gene phylogenies, while the luxS phylogeny was very similar to that of extant Bacillus spp. This suggests that luxS may have been acquired by horizontal transfer millions of years ago. Molecular clocks of luxS suggest slow evolutionary rates, similar to those of the 16S rRNA gene and consistent with a conserved gene.

The future of ancient DNA: Technical advances and conceptual shifts

“…Another field of research that has been revitalised by the introduction of NGS and hybridisation enrichment technologies is the study of ancient microbiota. DNA studies of ancient bacteria were highly controversial for many years , predominantly due to a lack of independent replication and authentication criteria, which would effectively screen for contamination from ubiquitous environmental microbes. More recent studies have shown that using both shotgun sequencing and hybridisation enrichment approaches it is possible to obtain (more) reliable genetic information from palaeopathogens .…”

Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology

“…have also been isolated from 23- to 35-million-year-old and 120-million-year-old amber, respectively (61–63). Even more unexpected was the isolation of Gram-negative bacteria resembling Brevundimonas in 25- to 40-million-year-old amber (64). The isolation of a Gram-negative, non-spore-forming bacterium suggests that microbes have an array of currently unknown mechanisms that could be involved in their long-term survival.…”

“…Currently, the specific molecular mechanisms by which microbes isolated from amber become dormant and are resuscitated after millions of years are being further investigated. Amplification of genes such as rpf , which stands for resuscitation promoting factor, and luxS , a gene involved in quorum sensing, may suggest that genes identified in extant bacteria may be involved in the survival of ancient microorganisms, including those preserved in amber (63, 64). …”

“…Furthermore, experimental design should accommodate the growth of both expected and unexpected microorganisms based on sample type (46, 59). However difficult and seemingly unlikely, increasing numbers of attempts have successfully resuscitated microorganisms from prehistoric amber and permafrost samples (50, 64). Similar studies have pinpointed possible key genes in the resuscitation process, including those for various proteins that act as resuscitation-promoting factors (62, 80, 81).…”

Reply to Santiago-Rodriguezet al.: WasluxSreally isolated from 25- to 40-million-year-old bacteria?

“…Although Santiago-Rodriguez et al (2014) attempt to reconstruct the evolutionary history of bacterial quorum sensing, the authors fail to address previous criticisms of this work and do not provide the appropriate experimental controls and analyses required to make the claims put forth in this article.…”