2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis

Earth's earliest biosphere-a proposal to develop a collection of curated archean geologic reference materials

The discovery of evidence indicative of life in a Martian meteorite has led to an increase in interest in astrobiology. As a result of this discovery, and the ensuing controversy, it has become apparent that our knowledge of the early development of life on Earth is limited. Archean stratigraphic successions containing evidence of Earth's early biosphere are well preserved in the Pilbara Craton of Western Australia. The craton includes part of a protocontinent consisting of granitoid complexes that were emplaced into, and overlain by, a 3.51-2.94 Ga volcanigenic carapace - the Pilbara Supergroup. The craton is overlain by younger supracrustal basins that form a time series recording Earth history from approximately 2.8 Ga to approximately 1.9 Ga. It is proposed that a well-documented suite of these ancient rocks be collected as reference material for Archean and astrobiological research. All samples would be collected in a well-defined geological context in order to build a framework to test models for the early evolution of life on Earth and to develop protocols for the search for life on other planets.

The origin and evolution of model organisms

The phylogeny and timescale of life are becoming better understood as the analysis of genomic data from model organisms continues to grow. As a result, discoveries are being made about the early history of life and the origin and development of complex multicellular life. This emerging comparative framework and the emphasis on historical patterns is helping to bridge barriers among organism-based research communities.

Questioning the evidence for Earth's oldest fossils

Structures resembling remarkably preserved bacterial and cyanobacterial microfossils from about 3,465-million-year-old Apex cherts of the Warrawoona Group in Western Australia currently provide the oldest morphological evidence for life on Earth and have been taken to support an early beginning for oxygen-producing photosynthesis. Eleven species of filamentous prokaryote, distinguished by shape and geometry, have been put forward as meeting the criteria required of authentic Archaean microfossils, and contrast with other microfossils dismissed as either unreliable or unreproducible. These structures are nearly a billion years older than putative cyanobacterial biomarkers, genomic arguments for cyanobacteria, an oxygenic atmosphere and any comparably diverse suite of microfossils. Here we report new research on the type and re-collected material, involving mapping, optical and electron microscopy, digital image analysis, micro-Raman spectroscopy and other geochemical techniques. We reinterpret the purported microfossil-like structure as secondary artefacts formed from amorphous graphite within multiple generations of metalliferous hydrothermal vein chert and volcanic glass. Although there is no support for primary biological morphology, a Fischer--Tropsch-type synthesis of carbon compounds and carbon isotopic fractionation is inferred for one of the oldest known hydrothermal systems on Earth.

Building a multicellular organism

Multicellular organisms appear to have arisen from unicells numerous times. Multicellular cyanobacteria arose early in the history of life on Earth. Multicellular forms have since arisen independently in each of the kingdoms and several times in some phyla. If the step from unicellular to multicellular life was taken early and frequently, the selective advantage of multicellularity may be large. By comparing the properties of a multicellular organism with those of its putative unicellular ancestor, it may be possible to identify the selective force(s). The independent instances of multicellularity reviewed indicate that advantages in feeding and in dispersion are common. The capacity for signaling between cells accompanies the evolution of multicellularity with cell differentiation.

Mass-independent fractionation of sulfur isotopes in Archean sediments: strong evidence for an anoxic Archean atmosphere

Mass-independent fractionation (MIF) of sulfur isotopes has been reported in sediments of Archean and Early Proterozoic Age (> 2.3 Ga) but not in younger rocks. The only fractionation mechanism that is consistent with the data on all four sulfur isotopes involves atmospheric photochemical reactions such as SO2 photolysis. We have used a one-dimensional photochemical model to investigate how the isotopic fractionation produced during SO2 photolysis would have been transferred to other gaseous and particulate sulfur-bearing species in both low-O2 and high-O2 atmospheres. We show that in atmospheres with O2 concentrations < 10(-5) times the present atmospheric level (PAL), sulfur would have been removed from the atmosphere in a variety of different oxidation states, each of which would have had its own distinct isotopic signature. By contrast, in atmospheres with O2 concentrations > or = 10(-5) PAL, all sulfur-bearing species would have passed through the oceanic sulfate reservoir before being incorporated into sediments, so any signature of MIF would have been lost. We conclude that the atmospheric O2 concentration must have been < 10(-5) PAL prior to 2.3 Ga.

A genomic timescale for the origin of eukaryotes

BACKGROUND

Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis. However, details of the timing and number of symbiotic events are unclear. A timescale for the early evolution of eukaryotes would help to better understand the relationship between these biological events and changes in Earth's environment, such as the rise in oxygen. We used refined methods of sequence alignment, site selection, and time estimation to address these questions with protein sequences from complete genomes of prokaryotes and eukaryotes.

RESULTS

Eukaryotes were found to evolve faster than prokaryotes, with those eukaryotes derived from eubacteria evolving faster than those derived from archaebacteria. We found an early time of divergence (approximately 4 billion years ago, Ga) for archaebacteria and the archaebacterial genes in eukaryotes. Our analyses support at least two horizontal gene transfer events in the origin of eukaryotes, at 2.7 Ga and 1.8 Ga. Time estimates for the origin of cyanobacteria (2.6 Ga) and the divergence of an early-branching eukaryote that lacks mitochondria (Giardia) (2.2 Ga) fall between those two events.

CONCLUSIONS

We find support for two symbiotic events in the origin of eukaryotes: one premitochondrial and a later mitochondrial event. The appearance of cyanobacteria immediately prior to the earliest undisputed evidence for the presence of oxygen (2.4-2.2 Ga) suggests that the innovation of oxygenic photosynthesis had a relatively rapid impact on the environment as it set the stage for further evolution of the eukaryotic cell.

Analysis of intact bacteriohopanepolyols from methanotrophic bacteria by reversed-phase high-performance liquid chromatography-atmospheric pressure chemical ionisation mass spectrometry

Direct detection of most intact biohopanoids is not possible using conventional GC-MS techniques due to their highly functionalised and amphiphilic nature. Here we report the application of a new reversed-phase high-performance liquid chromatography method for the direct analysis of acetylated, intact bacteriohopanepolyols in solvent extracts of methanotrophic bacteria. Atmospheric pressure chemical ionisation mass spectrometric detection provides structural information relating to the number and types of functional groups present in the four biohopanoids detected: bacteriohopanetetrol, aminobacteriohopanetriol, -tetrol and -pentol. The method should facilitate the assessment of hopanoid composition of both bacteria and environmental samples.

Novel methylated triterpenoids of the gammacerane series from the nitrogen-fixing bacterium Bradyrhizobium japonicum USDA 110

The nitrogen-fixing, symbiotic root-nodule forming bacterium Bradyrhizobium japonicum USDA 110 contained gammacerane derivatives next to triterpenoids of the hopane series. Diploptene, diplopterol, 2 beta-methyldiplopterol, aminobacteriohopanetriol and adenosylhopane were accompanied by tetrahymanol and the corresponding novel methylated homologues 2 beta-methyltetrahymanol, 20 alpha-methyltetrahymanol, and 2 beta,20 alpha-dimethyltetrahymanol. Incorporation of [(2)H(3)]methyl-L-methionine indicated that the additional methyl groups originated from methionine, probably with S-adenosylmethionine acting as methyl donor, with retention of the three deuterium atoms. The simultaneous presence of hopane and gammacerane derivatives seems a characteristic feature of the genus Bradyrhizobium and the phylogenetically closely related Rhodopseudomonas palustris.

The habitat and nature of early life

Earth is over 4,500 million years old. Massive bombardment of the planet took place for the first 500-700 million years, and the largest impacts would have been capable of sterilizing the planet. Probably until 4,000 million years ago or later, occasional impacts might have heated the ocean over 100 degrees C. Life on Earth dates from before about 3,800 million years ago, and is likely to have gone through one or more hot-ocean 'bottlenecks'. Only hyperthermophiles (organisms optimally living in water at 80-110 degrees C) would have survived. It is possible that early life diversified near hydrothermal vents, but hypotheses that life first occupied other pre-bottleneck habitats are tenable (including transfer from Mars on ejecta from impacts there). Early hyperthermophile life, probably near hydrothermal systems, may have been non-photosynthetic, and many housekeeping proteins and biochemical processes may have an original hydrothermal heritage. The development of anoxygenic and then oxygenic photosynthesis would have allowed life to escape the hydrothermal setting. By about 3,500 million years ago, most of the principal biochemical pathways that sustain the modern biosphere had evolved, and were global in scope.

Antiquity of the biological sulphur cycle: evidence from sulphur and carbon isotopes in 2700 million-year-old rocks of the Belingwe Belt, Zimbabwe

Sulphur and carbon isotopic analyses on small samples of kerogens and sulphide minerals from biogenic and non-biogenic sediments of the 2.7 x 10(9) years(Ga)-old Belingwe Greenstone Belt (Zimbabwe) imply that a complex biological sulphur cycle was in operation. Sulphur isotopic compositions display a wider range of biological fractionation than hitherto reported from the Archaean. Carbon isotopic values in kerogen record fractionations characteristic of rubisco activity methanogenesis and methylotrophy and possibly anoxygenic photosynthesis. Carbon and sulphur isotopic fractionations have been interpreted in terms of metabolic processes in 2.7 Ga prokaryote mat communities, and indicate the operation of a diverse array of metabolic processes. The results are consistent with models of early molecular evolution derived from ribosomal RNA.

Isoprenoid biosynthesis: the evolution of two ancient and distinct pathways across genomes

Isopentenyl diphosphate (IPP) is the central intermediate in the biosynthesis of isoprenoids, the most ancient and diverse class of natural products. Two distinct routes of IPP biosynthesis occur in nature: the mevalonate pathway and the recently discovered deoxyxylulose 5-phosphate (DXP) pathway. The evolutionary history of the enzymes involved in both routes and the phylogenetic distribution of their genes across genomes suggest that the mevalonate pathway is germane to archaebacteria, that the DXP pathway is germane to eubacteria, and that eukaryotes have inherited their genes for IPP biosynthesis from prokaryotes. The occurrence of genes specific to the DXP pathway is restricted to plastid-bearing eukaryotes, indicating that these genes were acquired from the cyanobacterial ancestor of plastids. However, the individual phylogenies of these genes, with only one exception, do not provide evidence for a specific affinity between the plant genes and their cyanobacterial homologues. The results suggest that lateral gene transfer between eubacteria subsequent to the origin of plastids has played a major role in the evolution of this pathway.