Ancient Microorganisms Research Articles

Resurrected microorganisms: a plethora of resting bacteria underway for human interaction

Glaciers, which form due to the accumulation of snow, play a crucial role in providing freshwater resources, supporting river systems, and maintaining ecosystem stability. Pakistan is habitat to over 5000 glaciers, primarily located in the Hindukash, Himalaya, and Karakoram mountain ranges. Understanding the microbial communities thriving in these extreme environments becomes of utmost importance. These glaciers offer a unique perspective on extremophile adaptation, as they harbor microorganisms that are capable of surviving and thriving under harsh conditions. Glacial melting poses a significant threat to ancient microbiomes, potentially leading to the resurgence of epidemics and exposure of life to paleomicrobiota. Mostly glacial microbiome is evenly distributed and shows similar diversity. With the threat of resurrection of ages old microbiome and its incorporation into the waters have raised a major concern for revival of epidemics and exposure of life with paleanmicrobiota again. This has led the scientist to deeply observe the bacterial flora embedded in the cryonite holes of glaciers. This study aims to investigate the bacterial diversity within various glaciers of Pakistan using metagenomic techniques. Kamri, Burzil, Siachin, Baltoro, Shigar Basin, Biafo and Panama Glaciers designated from G1 to G7 respectively were chosen from Pakistan. Through rigorous physicochemical analyses, distinct characteristics among glaciers are revealed, including variations in temperature, depth, electrical conductivity, pH levels, and nutrient concentrations. The exploration of alpha diversity, employing metrics such as Chao1, Shannon, Simpson, and Inverse Simpson indices, offers valuable insights into the richness, evenness, and dominance of species within different samples. Beta diversity was calculated by using R software. The vegan package was used for NMSD, cluster and PCoA analysis based on Bray–Curtis distance. PCA analysis was done by using prcomp package from R software. Based on OTU abundance and environmental factor data, DCA analysis was done to determine the linear model from the gradient value (RDA) and the unimodal model (CCA). results were compiled by drawing cluster dendrogram which predicts the patterns of similarity and dissimilarity between different samples. Notably, phyla Proteobacteria emerge as the dominant phylum, accompanied by Actinobacteria, Firmicutes, and Bacteroidetes. The dendrogram shows five clusters, with close similarity between G1 and G4, glacier samples G3 and G8, and G2 and G7. Seasonal variations in glacier physicochemical properties were also observed, with summer samples having shallower depths, lower temperatures, and slightly acidic pH. In contrast, winter samples have higher electrical conductivity and sulfur content. Ultimately, this research provides a foundational framework for comprehending glacier ecosystems, their resident microbial communities, and their broader ecological significance. The study highlights the potential public health risks linked to the release of ancient microorganisms due to climate change, emphasizing the need for comprehensive monitoring and research to mitigate potential public health threats.

Time-travelling pathogens and their risk to ecological communities.

Permafrost thawing and the potential 'lab leak' of ancient microorganisms generate risks of biological invasions for today's ecological communities, including threats to human health via exposure to emergent pathogens. Whether and how such 'time-travelling' invaders could establish in modern communities is unclear, and existing data are too scarce to test hypotheses. To quantify the risks of time-travelling invasions, we isolated digital virus-like pathogens from the past records of coevolved artificial life communities and studied their simulated invasion into future states of the community. We then investigated how invasions affected diversity of the free-living bacteria-like organisms (i.e., hosts) in recipient communities compared to controls where no invasion occurred (and control invasions of contemporary pathogens). Invading pathogens could often survive and continue evolving, and in a few cases (3.1%) became exceptionally dominant in the invaded community. Even so, invaders often had negligible effects on the invaded community composition; however, in a few, highly unpredictable cases (1.1%), invaders precipitated either substantial losses (up to -32%) or gains (up to +12%) in the total richness of free-living species compared to controls. Given the sheer abundance of ancient microorganisms regularly released into modern communities, such a low probability of outbreak events still presents substantial risks. Our findings therefore suggest that unpredictable threats so far confined to science fiction and conjecture could in fact be powerful drivers of ecological change.

Oil Inclusions Found in Skeleton Crystals of Quartz Indicated the Existence of Organic Matter Surrounding Ancient Growth Environments.

In nature, minerals record various origins and information for geology and geobiochemistry. Here, we investigated the origin of organic matter and growth mechanism of quartz with oil inclusion revealing fluorescence under short ultraviolet (UV) light, obtained from the clay vein at Shimanto-cho, Kochi, Shikoku Island, Japan. Geological investigation indicated that the oil-quartz was formed in hydrothermal metamorphic veins found in the late Cretaceous interbedded sandstone and mudstone. The obtained oil-quartz crystals are mostly double-terminated. Micro-X-ray computed tomography (microCT) indicated that oil-quartz crystals have various veins originating as skeleton structures along the quartz crystal {111} and {1-11} faces. Spectroscopic and chromatographic studies indicated that aromatic ester and tetraterpene (lycopene) molecules, which revealed fluorescence, were detected. Large molecular weight sterol molecules, such as C40, were also detected in the vein of oil-quartz. This investigation indicated that organic inclusions in mineral crystals would form with ancient microorganism culture environments.

Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD.

In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.

Dark microbiome and extremely low organics in Atacama fossil delta unveil Mars life detection limits

Identifying unequivocal signs of life on Mars is one of the most important objectives for sending missions to the red planet. Here we report Red Stone, a 163-100 My alluvial fan–fan delta that formed under arid conditions in the Atacama Desert, rich in hematite and mudstones containing clays such as vermiculite and smectites, and therefore geologically analogous to Mars. We show that Red Stone samples display an important number of microorganisms with an unusual high rate of phylogenetic indeterminacy, what we refer to as “dark microbiome”, and a mix of biosignatures from extant and ancient microorganisms that can be barely detected with state-of-the-art laboratory equipment. Our analyses by testbed instruments that are on or will be sent to Mars unveil that although the mineralogy of Red Stone matches that detected by ground-based instruments on the red planet, similarly low levels of organics will be hard, if not impossible to detect in Martian rocks depending on the instrument and technique used. Our results stress the importance in returning samples to Earth for conclusively addressing whether life ever existed on Mars.

Ancient Microorganisms and Carotenoids Preserved in Fluid Inclusions in Halite from Chaka Salt Lake, Western China: Evidence from Micro‐observation and in situ Raman Spectroscopy

AbstractTrapped ancient microorganisms in halite fluid inclusions are of special interest to the understanding of biology and ecology in salt lake systems. With the integration of petrologic, microthermometric, and Raman spectroscopic analyses, this study utilizes fluid inclusions from Chaka Salt Lake, eastern Qaidam Basin, NW China, to assess the possibility of microorganism‐trapping by fluid inclusions. Here, we report that the solid phase of some primary fluid inclusions contains carotenoids, which is interpreted as evidence of Dunaliella algae, and that the coexisting liquid phase comprises SO42‐. The homogenization temperatures of single‐phase primary fluid inclusions indicate that the precipitation temperature of the Holocene halite in Chaka Salt Lake ranges from 13.5°C to 36.4°C. This suggests that fluid inclusions in halite are a good medium for trapping and preserving ancient microorganisms and organic matter in salt lakes, and that Raman spectroscopy has good potential to identify halophilic archaea.

BIOLOGICAL PROPERTY OF THE ECOLOGICAL CULTURES MYCOBACTERIUM VACCAE

Prokaryotes of the genus Mycobacterium occupy an important evolutionary and historical place in the system of microorganisms of prokaryotic and eukaryotic organization in the Earth's biosphere. These are the most ancient microorganisms that have passed a long historical path of mutual adaptation with the evolving biosphere over billions of years. Antiquity of origin is very important in the process of developing a stable and at the same time adaptive genomic apparatus, which provides genetic information support for the very diverse physiological needs of a carrier of a given genotype in the constantly changing conditions of the environment of existence and creating competitive advantages over similar carriers of gene programs in the limited space of a specific ecosystem.
 A significant species diversity of prokaryotes of the genus Mycobacterium is a consequence of the wide divergence of the ancestral ancestor species of the sapronous type in the process of soil formation from lithotrophic forms to the highest degree of bioparasitism in the form of highly specialized infectious pathogens with pronounced pathogenicity, invasiveness and the potential ability to take root in an internal macroorganism and an extremely effective antagonist the immune system of supervision over the genetic homeostasis of a macroorganism with a paradigm of tolerance to its genetically own and categorical intolerance to carriers of geneticaly foreign information.
 Only a small number of mycobacterial species have adapted to the internal environment of eukaryotic macroorganisms as a result of the suppression of the protective mechanisms of the lymphoid system by pathogenic factors. The path of symbiotic relationships, mutually beneficial interpopulation, turned out to be much more effective. As a result, a dynamic microbial organ arose - the microbiota of the large intestine, inhabited by indigenous and transient microbionts, among which Mycobacterium vaccae occupy an important place.
 Ecological strains "K", "N", "Gk", "Gn" of Mycobacterium vaccae were isolated and identified by conventional bacteriological methods. Examined their basic properties. The strains possessed morpho-tinctorial, cultural and biochemical properties characteristic of the species, were apathogenic for laboratory animals when administered parenterally, caused short-term sensitization to mycobacterial antigens and induced antitilogenesis. In broiler chickens on fattening with oral feeding of live culture, they stimulated metabolism, increased weight gain and increased the protective properties of the nonspecific link of the immune reactivity of the macroorganism.
 Strains of atypical mycobacteria were isolated on the territory of one poultry farm and had similar biocharacteristics; they are suitable for use as probiotics to increase nonspecific resistance, stimulate the physiological functions of the macroorganism, increase weight gain and improve feed payment.

Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation

Next Generation Sequencing (NGS) has unlocked access to the wide range of non-cultivable microorganisms, including those present in the ancient past. The study of microorganisms from ancient sources (palaeomicrobiology) using DNA sequencing now provides a unique opportunity to examine ancient microbial genomic content, explore pathogenicity, and understand microbial evolution in greater detail than ever before. As a result, current studies have focused on reconstructing the evolutionary history of a number of human pathogens involved in ancient and historic pandemic events. These studies have opened the door for a variety of future palaeomicrobiology studies, which can focus on commensal microorganisms, species from non-human hosts, information from host-genomics, and the use of bacteria as proxies for additional information about past human health, behavior, migration, and culture. Here, we describe the origin and the historical and recent advances in the field of palaeomicrobiology, review some of the most notable ancient pathogenic microorganism studies, and provide perspectives on how NGS and whole genome information from ancient microorganisms contribute to our understanding of bacterial evolution on a broader scale. We conclude by exploring the application of newly developed tools in palaeomicrobiology and discussing how future studies can improve our current understanding of the co-evolution relationships between humans and non-pathogenic microbes.

Comparative genomics analysis of c-di-GMP metabolism and regulation in Microcystis aeruginosa

BackgroundCyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically diverse habitats because of their capacity to rapidly respond to environmental changes through a web of complex signaling networks, including using second messengers to regulate physiology or metabolism. A ubiquitous second messenger, bis-(3′,5′)-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has been found to regulate essential behaviors in a few cyanobacteria but not Microcystis, which are the most dominant species in cyanobacterial blooms. In this study, comparative genomics analysis was performed to explore the genomic basis of c-di-GMP signaling in Microcystis aeruginosa.ResultsProteins involved in c-di-GMP metabolism and regulation, such as diguanylate cyclases, phosphodiesterases, and PilZ-containing proteins, were encoded in M. aeruginosa genomes. However, the number of identified protein domains involved in c-di-GMP signaling was not proportional to the size of M. aeruginosa genomes (4.97 Mb in average). Pan-genome analysis showed that genes involved in c-di-GMP metabolism and regulation are conservative in M. aeruginosa strains. Phylogenetic analysis showed good congruence between the two types of phylogenetic trees based on 31 highly conserved protein-coding genes and sensor domain-coding genes. Propensity for gene loss analysis revealed that most of genes involved in c-di-GMP signaling are stable in M. aeruginosa strains. Moreover, bioinformatics and structure analysis of c-di-GMP signal-related GGDEF and EAL domains revealed that they all possess essential conserved amino acid residues that bind the substrate. In addition, it was also found that all selected M. aeruginosa genomes encode PilZ domain containing proteins.ConclusionsComparative genomics analysis of c-di-GMP metabolism and regulation in M. aeruginosa strains helped elucidating the genetic basis of c-di-GMP signaling pathways in M. aeruginosa. Knowledge of c-di-GMP metabolism and relevant signal regulatory processes in cyanobacteria can enhance our understanding of their adaptability to various environments and bloom-forming mechanism.

Buried Soils as a New Source for Isolation of Biotechnologically Significant Bacterial Strains

Investigation of molecular genetic diversity in paleosoil microbial communities revealed that ~50% of ancient ribotypes were not detected among the ribotypes of the modern microbial communities. Thus, reactivation of ancient microorganisms and investigation of their physiological properties as potentially valuable producers for biotechnology is advisable. The proteolytic bacterial component of paleosoils below burial mounds collected from the vials with votive food at the Peschanyi-4 and Netkachevo burial mounds (15–centuries BC) (Volgograd and Rostov oblasts, Russia) was investigated. Viable cell numbers of heterotrophic bacteria in reactivated samples were (1.5–16.0) × 107 CFU/g soil (growth on LB agar). Using alternating inoculation into liquid media and plating on solid media resulted in isolation of pure cultures of several strains, which were then identified based on analysis of their 16S rRNA gene sequences. Strains of the following species were isolated: Bacillus coagulans (Lactobacillus coagulans), a potentially valuable probiotic; Aquamicrobium terrae, a proteolytic producing surfactants and degrading organic matter; Bacillus cereus, the strain toxicogenic for outbred white mice at intra-abdominal application; Staphylococcus hominis and St. epidermidis, opportunistic pathogens belonging to normal human skin microflora. Apart from Bacillus cereus, all strains exhibited high production of neuroactive amines (DOPA, DOPAC, DA, 5-HTP, HVA, and 3-MT) and amino acids (Asp, Glu, Gly, Tau, and GABA). The strains isolated from the vials with votive food were mostly those associated with humans, rather than typical members of soil microbial communities.

Assessing alignment-based taxonomic classification of ancient microbial DNA.

The field of palaeomicrobiology—the study of ancient microorganisms—is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.

Geochemistry and the Origin of Life: From Extraterrestrial Processes, Chemical Evolution on Earth, Fossilized Life's Records, to Natures of the Extant Life.

In 2001, the first author (S.N.) led the publication of a book entitled “Geochemistry and the origin of life” in collaboration with Dr. Andre Brack aiming to figure out geo- and astro-chemical processes essential for the emergence of life. Since then, a great number of research progress has been achieved in the relevant topics from our group and others, ranging from the extraterrestrial inputs of life’s building blocks, the chemical evolution on Earth with the aid of mineral catalysts, to the fossilized records of ancient microorganisms. Here, in addition to summarizing these findings for the origin and early evolution of life, we propose a new hypothesis for the generation and co-evolution of photosynthesis with the redox and photochemical conditions on the Earth’s surface. Besides these bottom-up approaches, we introduce an experimental study on the role of water molecules in the life’s function, focusing on the transition from live, dormant, and dead states through dehydration/hydration. Further spectroscopic studies on the hydrogen bonding behaviors of water molecules in living cells will provide important clues to solve the complex nature of life.

Morphophysiological and transcriptome analysis reveals a multiline defense system enabling cyanobacterium Leptolyngbya strain JSC-1 to withstand iron induced oxidative stress

Iron intoxications induce severe oxidative stress by producing reactive oxygen species (ROS) in cyanobacteria, leading to membrane lipid peroxidation, altered morphology, impaired photosynthesis and other oxidative stress injuries. Given these stresses, mitigation of ROS is a prerequisite for all aerobic organisms. Study of siderophilic cyanobacterium Leptolyngbya strain JSC-1 inhabiting iron-rich hot springs may provide insight into the mechanism of iron homeostasis and alleviation of oxidative stress. In this study, we investigated the morphophysiological and molecular mechanisms enabling this cyanobacterium to cope with iron-induced oxidative stress. Strain JSC-1 biomineralized extracellular iron via an exopolymeric sheath (acting as a first line of defense) and intracellular iron via polyphosphate inclusions (second line of defense), thus minimizing the burden of free ferric ions. Physiological parameters, SOD, CAT and POD activities, bacterioferritin and total protein contents fluctuated in response to iron elevation, displaying a third line of defense to mitigate ROS. Differential gene expression analysis of JSC-1 indicated up-regulation of 94 and 125 genes and down-regulation of 89 and 183 genes at low (4 μM) and high (400 μM) iron concentration, respectively. The differentially expressed genes (DEGs) were enriched in 100 KEGG pathways and were found to be involved in lipopolysaccharide and fatty acid biosynthesis, starch, sucrose, chlorophyll and other metabolic pathways. Together with metabolic reprogramming (fourth line of defense), JSC-1 established a unique multiline defense system that allows JSC-1 to withstand severe oxidative stress. These findings also provide insight into potential survival strategies of ancient microorganisms inhabiting similar environment present in early earth history.

Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy.

Diet is one of the main factors that affects the composition of gut microbiota. When people move from a rural environment to urban areas, and experience improved socio-economic conditions, they are often exposed to a “globalized” Western type diet. Here, we present preliminary observations on the metagenomic scale of microbial changes in small groups of African children belonging to the same ethnicity and living in different environments, compared to children living on the urban area of Florence (Italy). We analyzed dietary habits and, by pyrosequencing of the 16S rRNA gene, gut microbiota profiles from fecal samples of children living in a rural village of Burkina Faso (n = 11), of two groups of children living in different urban settings (Nanoro town, n = 8; Ouagadougou, the capital city, n = 5) and of a group of Italian children (n = 13). We observed that when foods of animal origin, those rich in fat and simple sugars are introduced into a traditional African diet, composed of cereals, legumes and vegetables, the gut microbiota profiles changes. Microbiota of rural children retain a geographically unique bacterial reservoir (Prevotella, Treponema, and Succinivibrio), assigned to ferment fiber and polysaccharides from vegetables. Independently of geography and ethnicity, in children living in urban areas these bacterial genera were progressively outcompeted by bacteria more suited to the metabolism of animal protein, fat and sugar rich foods, similarly to Italian children, as resulted by PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), a predictive functional profiling of microbial communities using 16S rRNA marker gene. Consequently, we observed a progressive reduction of SCFAs measured by gas chromatography–mass spectrometry, in urban populations, especially in Italian children, respect to rural ones. Our results even if in a limited number of individuals point out that dietary habit modifications in the course of urbanization play a role in shaping gut microbiota, and that ancient microorganisms, such as fiber-degrading bacteria, are at risk of being eliminated by the fast paced globalization of foods and by the advent of westernized lifestyle.

Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico.

BackgroundThe study of ancient microorganisms in mineralized dental plaque or calculi is providing insights into microbial evolution, as well as lifestyles and disease states of extinct cultures; yet, little is still known about the oral microbial community structure and function of pre-Columbian Caribbean cultures. In the present study, we investigated the dental calculi microbiome and predicted function of one of these cultures, known as the Saladoid. The Saladoids were horticulturalists that emphasized root-crop production. Fruits, as well as small marine and terrestrial animals were also part of the Saladoid diet.MethodsDental calculi samples were recovered from the archaeological site of Sorcé, in the municipal island of Vieques, Puerto Rico, characterized using 16S rRNA gene high-throughput sequencing, and compared to the microbiome of previously characterized coprolites of the same culture, as well modern plaque, saliva and stool microbiomes available from the Human Microbiome Project.ResultsActinobacteria, Proteobacteria and Firmicutes comprised the majority of the Saladoid dental calculi microbiome. The Saladoid dental calculi microbiome was distinct when compared to those of modern saliva and dental plaque, but showed the presence of common inhabitants of modern oral cavities including Streptococcus sp., Veillonella dispar and Rothia mucilaginosa. Cell motility, signal transduction and biosynthesis of other secondary metabolites may be unique features of the Saladoid microbiome.DiscussionResults suggest that the Saladoid dental calculi microbiome structure and function may possibly reflect a horticulturalist lifestyle and distinct dietary habits. Results also open the opportunity to further elucidate oral disease states in extinct Caribbean cultures and extinct indigenous cultures with similar lifestyles.

Ancient permafrost staphylococci carry antibiotic resistance genes.

ABSTRACTBackground: Permafrost preserves a variety of viable ancient microorganisms. Some of them can be cultivated after being kept at subzero temperatures for thousands or even millions of years.Objective: To cultivate bacterial strains from permafrost.Design: We isolated and cultivated two bacterial strains from permafrost that was obtained at Mammoth Mountain in Siberia and attributed to the Middle Miocene. Bacterial genomic DNA was sequenced with 40–60× coverage and high-quality contigs were assembled. The first strain was assigned to Staphylococcus warneri species (designated MMP1) and the second one to Staphylococcus hominis species (designated MMP2), based on the classification of 16S ribosomal RNA genes and genomic sequences.Results: Genomic sequence analysis revealed the close relation of the isolated ancient bacteria to the modern bacteria of this species. Moreover, several genes associated with resistance to different groups of antibiotics were found in the S. hominis MMP2 genome.Conclusions: These findings supports a hypothesis that antibiotic resistance has an ancient origin. The enrichment of cultivated bacterial communities with ancient permafrost strains is essential for the analysis of bacterial evolution and antibiotic resistance.

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

Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.

Starvation-Survival in Haloarchaea.

Recent studies claiming to revive ancient microorganisms trapped in fluid inclusions in halite have warranted an investigation of long-term microbial persistence. While starvation-survival is widely reported for bacteria, it is less well known for halophilic archaea—microorganisms likely to be trapped in ancient salt crystals. To better understand microbial survival in fluid inclusions in ancient evaporites, laboratory experiments were designed to simulate growth of halophilic archaea under media-rich conditions, complete nutrient deprivation, and a controlled substrate condition (glycerol-rich) and record their responses. Haloarchaea used for this work included Hbt. salinarum and isolate DV582A-1 (genus Haloterrigena) sub-cultured from 34 kyear Death Valley salt. Hbt. salinarum and DV582A-1 reacted to nutrient limitation with morphological and population changes. Starved populations increased and most cells converted from rods to small cocci within 56 days of nutrient deprivation. The exact timing of starvation adaptations and the physical transformations differed between species, populations of the same species, and cells of the same population. This is the first study to report the timing of starvation strategies for Hbt. salinarum and DV582A-1. The morphological states in these experiments may allow differentiation between cells trapped with adequate nutrients (represented here by early stages in nutrient-rich media) from cells trapped without nutrients (represented here by experimental starvation) in ancient salt. The hypothesis that glycerol, leaked from Dunaliella, provides nutrients for the survival of haloarchaea trapped in fluid inclusions in ancient halite, is also tested. Hbt. salinarum and DV582A-1 were exposed to a mixture of lysed and intact Dunaliella for 56 days. The ability of these organisms to utilize glycerol from Dunaliella cells was assessed by documenting population growth, cell length, and cell morphology. Hbt. salinarum and DV582A-1 experienced size reductions and shape transitions from rods to cocci. In the short-term, these trends more closely resembled the response of these organisms to starvation conditions than to nutrient-rich media. Results from this experiment reproduced the physical state of cells (small cocci) in ancient halite where prokaryotes co-exist with single-celled algae. We conclude that glycerol is not the limiting factor in the survival of haloarchaea for thousands of years in fluid inclusions in halite.

A new approach to ancient microorganisms: taxonomy, paleoecology, and biostratigraphy of the Lower Cambrian Berkuta and Chulaktau microbiotas of South Kazakhstan

AbstractPeritidal cherts and silicified phosphorites of the Early Cambrian Kyrshabakta (Berkuta Member) and Chulaktau formations of South Kazakhstan contain diverse assemblages of cellularly permineralized microorganisms that like other microbiotas of similar age and setting are dominated by cyanobacteria, both filamentous (oscillatoriacean trichomes and empty sheaths) and coccoidal (chroococcaceans). Although these near-shore assemblages contain sphaeromorph acritarchs, they differ from Neoproterozoic and Early Cambrian microbiotas of more open-marine environments by lacking morphologically complex planktonic eukaryotes such as the acanthomorphic acritarchs that are abundant in the Chulaktau-overlying Shabakta Formation. In general composition, the Berkuta and Chulaktau assemblages are similar both to microfossil assemblages of the pre-trilobite Rovno and Lontova Regional Stages of the East European Platform and to Early Cambrian microbiotas known from chert-phosphorite deposits worldwide.The studies reported here are based on use of optical microscopy combined with techniques recently introduced to paleobiology: confocal laser scanning microscopy, and Raman and fluorescence spectroscopy and imagery. Taken together, these provide information in situ, in three dimensions and at high spatial resolution, about the organismal morphology; cellular anatomy; chemical composition; and mode, fidelity, and environment of preservation of the permineralized microfossils. Data are presented suggesting that the substitution of samarium for calcium in fossil-preserving apatite may provide evidence of its oxic or anoxic paleoenvironment of formation.We interpret the Berkuta and Chulaktau assemblages to be composed of 27 taxa assigned to 17 genera of microscopic prokaryotes and eukaryotes that include one new genus and species, Berkutaphycus elongatus.

Extragastric manifestations of Helicobacter pylori infection: Possible role of bacterium in liver and pancreas diseases.

Helicobacter pylori (H. pylori) is an ancient microorganism that has co-evolved with humans for over 60000 years. This bacterium typically colonizes the human stomach and it is currently recognized as the most common infectious pathogen of the gastroduodenal tract. Although its chronic infection is associated with gastritis, peptic ulcer, dysplasia, neoplasia, MALT lymphoma and gastric adenocarcinoma, it has been suggested the possible association of H. pylori infection with several extragastric effects including hepatobiliary and pancreatic diseases. Since a microorganism resembling H. pylori was detected in samples from patients with hepatobiliary disorders, several reports have been discussed the possible role of bacteria in hepatic diseases as hepatocellular carcinoma, cirrhosis and hepatic encephalopathy, nonalcoholic fatty liver disease and fibrosis. Additionally, studies have reported the possible association between H. pylori infection and pancreatic diseases, especially because it has been suggested that this infection could change the pancreatic physiology. Some of them have related a possible association between the microorganism and pancreatic cancer. H. pylori infection has also been suggested to play a role in the acute and chronic pancreatitis pathogenesis, autoimmune pancreatitis, diabetes mellitus and metabolic syndrome. Considering that association of H. pylori to liver and pancreas diseases needs further clarification, our work offers a review about the results of some investigations related to the potential pathogenicity of H. pylori in these extragastric diseases.