Modern Microbes Research Articles

Calcimicrobes in Cambrian microbialites (Shandong, North China) and comparison with experimentally produced biomineralization precipitates

Microbialites can be important oil and gas reservoirs because of their high initial porosity and they may well be source rocks too. However, the formation mechanisms of calcimicrobes in microbialites are still not fully understood, and further research is needed. Herein, microbialites (thrombolites, dendrolites, and oncolites) from the Cambrian successions of Shandong Province, China, are examined for their microbial fabrics and comparisons are made with the results of laboratory biomineralization experiments using the modern cyanobacterium Synechocystis sp. PCC6803 and the halophilic Bacillus licheniformis SRB2. The thrombolites show mosaic, meshed, and spotted textures, each with a different microbial clot morphology, and Epiphyton is the dominant calcimicrobe. Dendrolitic buildups consist of a lower gray core dominated by the chambered Renalcis, and an upper orange part dominated by dendritic Epiphyton, suggesting a transition of the microbial community across the color change, related to an increase in iron content. Oncolites occur in beds up to 10-cm-thick with spherical to ellipsoidal oncoids containing Girvanella developed around a bioclast nucleus. Scanning electron microscopy observations distinguish the calcimicrobes with their rough, peloidal surface morphology from adjacent cement; aggregated spheroidal and or filamentous calcimicrobes can be recognized, the latter with hollow centers in some cases. The results of the laboratory biomineralization experiments show that the two modern microbes can induce the precipitation of carbonate minerals, mostly of calcite. These biominerals are commonly granular and have a complex microscopic structure including spherical and dumbbell shapes. The microbes are commonly encrusted with calcite and after decomposition of the bacteria, hollow mineral crusts are produced; these are the result of the nucleation and growth of nano-minerals on the extracellular polymeric substances (EPS) present around the microbes. The bio-precipitates induced by modern microbes in the laboratory experiments are similar in many respects to the calcimicrobes in the Cambrian microbialites; biomineralization processes clearly play an important role in the formation of carbonate minerals and lithification of microbial mats.

Voltage vs. Ligand II: Structural insights of the intrinsic flexibility in cyclic nucleotide-gated channels

ABSTRACTIn the preceding article, we present a flexibility analysis of the voltage-gated ion channel (VGIC) superfamily. In this study, we describe in detail the flexibility profile of the voltage-sensor domain (VSD) and the pore domain (PD) concerning the evolution of 6TM ion channels. In particular, we highlight the role of flexibility in the emergence of CNG channels and describe a significant level of sequence similarity between the archetypical VSD and the TolQ proteins. A highly flexible S4-like segment exhibiting Lys instead Arg for these membrane proteins is reported. Sequence analysis indicates that, in addition to this S4-like segment, TolQ proteins also show similarity with specific motifs in S2 and S3 from typical V-sensors. Notably, S3 flexibility profiles from typical VSDs and S3-like in TolQ proteins are also similar. Interestingly, TolQ from early divergent prokaryotes are comparatively more flexible than those in modern counterparts or true V-sensors. Regarding the PD, we also found that 2TM K+-channels in early prokaryotes are considerably more flexible than the ones in modern microbes, and such flexibility is comparable to the one present in CNG channels. Voltage dependence is mainly exhibited in prokaryotic CNG channels whose VSD is rigid whereas the eukaryotic CNG channels are considerably more flexible and poorly V-dependent. The implication of the flexibility present in CNG channels, their sensitivity to cyclic nucleotides and the cation selectivity are discussed. Finally, we generated a structural model of the putative cyclic nucleotide-modulated ion channel, which we coined here as AqK, from the thermophilic bacteria Aquifex aeolicus, one of the earliest diverging prokaryotes known. Overall, our analysis suggests that V-sensors in CNG-like channels were essentially rigid in early prokaryotes but raises the possibility that this module was probably part of a very flexible stator protein of the bacterial flagellum motor complex.

Native iron reduces CO2 to intermediates and end-products of the acetyl-CoA pathway.

Autotrophic theories for the origin of life propose that CO2 was the carbon source for primordial biosynthesis. Among the six known CO2 fixation pathways in nature, the acetyl CoA (or Wood-Ljungdahl) pathway is the most ancient, and relies on transition metals for catalysis. Modern microbes that use the acetyl CoA pathway typically fix CO2 with electrons from H2, which requires complex flavin-based electron bifurcation. This presents a paradox: How could primitive metabolic systems have fixed CO2 before the origin of proteins? Here we show that native transition metals (Fe0, Ni0, Co0) selectively reduce CO2 to acetate and pyruvate, the intermediates and end-products of the AcCoA pathway, in near mM levels in water over hours to days using 1-40 bar CO2 and at temperatures from 30-100 °C. Geochemical CO2 fixation from native metals could have supplied critical C2 and C3 metabolites before the emergence of enzymes.

Planktonic marine iron oxidizers drive iron mineralization under low-oxygen conditions.

Observations of modern microbes have led to several hypotheses on how microbes precipitated the extensive iron formations in the geologic record, but we have yet to resolve the exact microbial contributions. An initial hypothesis was that cyanobacteria produced oxygen which oxidized iron abiotically; however, in modern environments such as microbial mats, where Fe(II) and O2 coexist, we commonly find microaerophilic chemolithotrophic iron-oxidizing bacteria producing Fe(III) oxyhydroxides. This suggests that such iron oxidizers could have inhabited niches in ancient coastal oceans where Fe(II) and O2 coexisted, and therefore contributed to banded iron formations (BIFs) and other ferruginous deposits. However, there is currently little evidence for planktonic marine iron oxidizers in modern analogs. Here, we demonstrate successful cultivation of planktonic microaerophilic iron-oxidizing Zetaproteobacteria from the Chesapeake Bay during seasonal stratification. Iron oxidizers were associated with low oxygen concentrations and active iron redox cycling in the oxic-anoxic transition zone (<3μm O2 , <0.2μm H2 S). While cyanobacteria were also detected in this transition zone, oxygen concentrations were too low to support significant rates of abiotic iron oxidation. Cyanobacteria may be providing oxygen for microaerophilic iron oxidation through a symbiotic relationship; at high Fe(II) levels, cyanobacteria would gain protection against Fe(II) toxicity. A Zetaproteobacteria isolate from this site oxidized iron at rates sufficient to account for deposition of geologic iron formations. In sum, our results suggest that once oxygenic photosynthesis evolved, microaerophilic chemolithotrophic iron oxidizers were likely important drivers of iron mineralization in ancient oceans.

Magnetite compensates for the lack of a pilin‐associated c‐type cytochrome in extracellular electron exchange

Nanoscale magnetite can facilitate microbial extracellular electron transfer that plays an important role in biogeochemical cycles, bioremediation and several bioenergy strategies, but the mechanisms for the stimulation of extracellular electron transfer are poorly understood. Further investigation revealed that magnetite attached to the electrically conductive pili of Geobacter species in a manner reminiscent of the association of the multi-heme c-type cytochrome OmcS with the pili of Geobacter sulfurreducens. Magnetite conferred extracellular electron capabilities on an OmcS-deficient strain unable to participate in interspecies electron transfer or Fe(III) oxide reduction. In the presence of magnetite wild-type cells repressed expression of the OmcS gene, suggesting that cells might need to produce less OmcS when magnetite was available. The finding that magnetite can compensate for the lack of the electron transfer functions of a multi-heme c-type cytochrome has implications not only for the function of modern microbes, but also for the early evolution of microbial electron transport mechanisms.

Ribosomal RNA gene fragments from fossilized cyanobacteria identified in primary gypsum from the late Miocene, Italy

Earth scientists have searched for signs of microscopic life in ancient samples of permafrost, ice, deep-sea sediments, amber, salt and chert. Until now, evidence of cyanobacteria has not been reported in any studies of ancient DNA older than a few thousand years. Here, we investigate morphologically, biochemically and genetically primary evaporites deposited in situ during the late Miocene (Messinian) Salinity Crisis from the north-eastern Apennines of Italy. The evaporites contain fossilized bacterial structures having identical morphological forms as modern microbes. We successfully extracted and amplified genetic material belonging to ancient cyanobacteria from gypsum crystals dating back to 5.910-5.816 Ma, when the Mediterranean became a giant hypersaline brine pool. This finding represents the oldest ancient cyanobacterial DNA to date. Our clone library and its phylogenetic comparison with present cyanobacterial populations point to a marine origin for the depositional basin. This investigation opens the possibility of including fossil cyanobacterial DNA into the palaeo-reconstruction of various environments and could also be used to quantify the ecological importance of cyanobacteria through geological time. These genetic markers serve as biosignatures providing important clues about ancient life and begin a new discussion concerning the debate on the origin of late Miocene evaporites in the Mediterranean.

Food Safety: Old Habits, New Perspectives

Anyone who works in food safety sooner or later discovers that one of the most valuable tools for prevention is simply reading about and understanding how past outbreaks have occurred. Using major and frequently famous or at least newsworthy outbreaks, Phyllis Entis in Food Safety: Old Habits, New Perspectives illustrates how critical factors come together to produce tragic and largely preventable results. This nicely written reference book reads more like an engaging novel in some ways, complete with bad guys (pathogens and sometimes careless corporations) and good guys (intrepid and resourceful outbreak investigators). The author’s unique style, usually avoided in science writing but appropriately used here, tells the tale of modern food safety issues so well that the book, literally, is difficult to put down. Each of the 17 chapters covers a different food safety principle, illuminating how modern microbes often team up with old practices, short-sighted decisions, or current consumer trends to produce an outbreak. Chapters conclude with a concise “lessons learned” summary, such as this conclusion from Chapter 3: “Whether it’s serotype Enteritidis in eggs or C. botulinum in eggplant, the challenge is the same. Recipes that do not include an adequate final cooking step have become increasingly popular with consumers and can be a significant source of food-borne illness.” One of the few downsides of this book is that it does leave the reader with the somewhat sensational impression that most food businesses are out to get the consumer. While the examples of greed and negligence are true, positive examples of good corporate behavior could have illustrated prevention and better balanced the portrayal of the food industry. Despite this small drawback, the tables are “one-stop shopping” for anyone looking for lists of outbreaks, and the fact boxes inserted here and there provide marvelous tidbits of information. A “who’s who” of microbes at the end of the book is an added bonus. Whether someone is preparing to teach a food safety course, looking for information about how and why outbreaks occur, or trying to get the facts on a critical food safety event, this author has already done all of the homework. For any food safety professional who has ever dreamed of the ultimate literature search, the references at the end of each chapter are breathtaking. This book is a must-have for any serious food safety professional.

Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution

The amount of lateral gene transfer (LGT) that has occurred in microbial evolution is heavily debated. Efforts to quantify LGT through gene-tree comparisons have delivered estimates that between 2% and 60% of all prokaryotic genes have been affected by LGT, the 30-fold discrepancy reflecting differences among gene samples studied and uncertainties inherent in phylogenetic reconstruction. Here we present a simple method that is independent of gene-tree comparisons to estimate the LGT rate among sequenced prokaryotic genomes. If little or no LGT has occurred during evolution, ancestral genome sizes would become unrealistically large, whereas too much LGT would render them far too small. We determine the amount of LGT that is necessary and sufficient to bring the distribution of inferred ancestral genome sizes into agreement with that observed among modern microbes. Rather than testing for phylogenetic congruence or lack thereof across genes, we assume that all gene trees are compatible; hence, our method delivers very conservative lower-bound estimates of the average LGT rate. The results indicate that among 57,670 gene families distributed across 190 sequenced genomes, at least two-thirds and probably all, have been affected by LGT at some time in their evolutionary past. A component of common ancestry nonetheless remains detectable in gene distribution patterns. We estimate the minimum lower bound for the average LGT rate across all genes as 1.1 LGT events per gene family and gene family lifespan and this minimum rate increases sharply when genes present in only a few genomes are excluded from the analysis.

Fatty acid and DNA analyses of Permian bacteria isolated from ancient salt crystals reveal differences with their modern relatives

The isolation of living microorganisms from primary 250-million-year-old (MYA) salt crystals has been questioned by several researchers. The most intense discussion has arisen from questions about the texture and age of the crystals used, the ability of organisms to survive 250 million years when exposed to environmental factors such as radiation and the close similarity between 16S rRNA sequences in the Permian and modern microbes. The data in this manuscript are not meant to provide support for the antiquity of the isolated bacterial strains. Rather, the data presents several comparisons between the Permian microbes and other isolates to which they appear related. The analyses include whole cell fatty acid profiling, DNA-DNA hybridizations, ribotyping, and random amplified polymorphic DNA amplification (RAPD). These data show that the Permian strains, studied here, differ significantly from their more modern relatives. These differences are accumulating in both phenotypic and molecular areas of the cells. At the fatty acid level the differences are approaching but have not reached separate species status. At the molecular level the variation appears to be distributed across the genome and within the gene regions flanking the highly conserved 16S rRNA itself. The data show that these bacteria are not identical and help to rule out questions of contamination by putatively modern strains.

Microbiology, Developmental Genetics and Evolution

The major elementary components of development in higher forms, that is, cellular division, cellular differentiation and epigenetic homeostasis, are well established in microorganisms. Their existence and functional significance in modern microbes suggest that they may all have arisen in primitive unicellular forms and may have provided the "pre-adaptive" basis for the transition to multicellularity. Regardless of whether the developmental mechanisms in unicellular and multicellular organisms are parts of a single evolutionary sequence or represent parallel evolutionary advances, modern experimental analyses emphasize their essential similarities. Nuclear differentiation, the regulation of genetic activities by modifications at particular chromosomal sites, may prove to be an important unifying concept. In any case, broad comparative studies on a variety of forms, selected for their suitability in exploring particular problems, should cross-illuminate each other and provide eventually the foundation for a "synthetic" developmental biology.