Evidence of Terrestrial Life From Archean Paleosols

Archean coastal-plain paleosols and life on land

Authors:

Retallack et al

Abstract:

Coastal-plain paleosols in the 3.0 Ga Farrel Quartzite of Western Australia have organic surface (A horizon) and sulfate-rich subsurface (By) horizons, like soils of the Atacama Desert of Chile, Dry Valleys of Antarctica, and 3.7 Ga paleosols of Mars. Farrel Quartzite paleosols include previously described microfossils, permineralized by silica in a way comparable with the Devonian Rhynie Chert, a well known permineralized Histosol. Five microfossil morphotypes in the Farrel Quartzite include a variety of spheroidal cells (Archaeosphaeroides) as well as distinctive large spindles (new genus provisionally assigned to cf. Eopoikilofusa). Previously published cell-specific carbon isotopic analyses of the Farrel Quartzite microfossils, and unusually abundant sulfate considering a likely anoxic atmosphere, allow interpretation of these morphotypes as a terrestrial community of actinobacteria, purple sulfur bacteria, and methanogenic Archaea.

Hadesarchaea: a new Extremophile Discovered Kilometers Deep in the Earth's Crust

They live several kilometers under the surface of the earth, need no light or oxygen and can only be seen in a microscope. By sequencing genomes of a newly discovered group of microbes, the Hadesarchaea, an international team of researchers have found out how these microorganisms make a living in the deep subsurface biosphere of our planet.

Microorganisms that live below the surface of the earth remain one of the last great areas of exploration. Organisms that live there have not been grow in the laboratory and therefore their lifestyles are unknown. An international team led by microbiologists Brett Baker, Assistant Professor at The University of Texas and Thijs Ettema, senior lecturer at Uppsala University, along with scientists from UNC Chapel Hill and the University of Bremen, have discovered how microorganisms, first discovered in a South African gold mine at a depth of two miles, are able to make a living in the absence of oxygen and light. The study is published in Nature Microbiology.

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New Phylogeny for Life Tied to Analysis of Archaea

The two-domain tree of life is linked to a new root for the Archaea

Authors:

Raymann et al

Abstract:

One of the most fundamental questions in evolutionary biology is the origin of the lineage leading to eukaryotes. Recent phylogenomic analyses have indicated an emergence of eukaryotes from within the radiation of modern Archaea and specifically from a group comprising Thaumarchaeota/“Aigarchaeota” (candidate phylum)/Crenarchaeota/Korarchaeota (TACK). Despite their major implications, these studies were all based on the reconstruction of universal trees and left the exact placement of eukaryotes with respect to the TACK lineage unclear. Here we have applied an original two-step approach that involves the separate analysis of markers shared between Archaea and eukaryotes and between Archaea and Bacteria. This strategy allowed us to use a larger number of markers and greater taxonomic coverage, obtain high-quality alignments, and alleviate tree reconstruction artifacts potentially introduced when analyzing the three domains simultaneously. Our results robustly indicate a sister relationship of eukaryotes with the TACK superphylum that is strongly associated with a distinct root of the Archaea that lies within the Euryarchaeota, challenging the traditional topology of the archaeal tree. Therefore, if we are to embrace an archaeal origin for eukaryotes, our view of the evolution of the third domain of life will have to be profoundly reconsidered, as will many areas of investigation aimed at inferring ancestral characteristics of early life and Earth.

Archaea Relative to Modern Eukaryotes Found

In a new study, published in Nature this week, a research team led from Uppsala University in Sweden presents the discovery of a new microbe that represents a missing link in the evolution of complex life. The study provides a new understanding of how, billions of years ago, the complex cell types that comprise plants, fungi, but also animals and humans, evolved from simple microbes.

Cells are the basic building blocks of all life on our planet. Yet, whereas the cells of bacteria and other microbes are small and simple, all visible life, including us humans, is generally made up of large and complex cell types. The origin of these complex cell types has long been a mystery to the scientific community, but now researchers from Uppsala University in Sweden have discovered a new group of microorganisms that represents a missing link in the evolutionary transition from simple to complex cells.

In the 1970s, the acclaimed biologist Carl Woese discovered a completely new group of microorganisms, the Archaea, and showed that these represented a separate branch in the Tree of Life -- a finding that stunned the scientific community at the time. Despite that archaeal cells were simple and small like bacteria, researchers found that Archaea were more closely related to organisms with complex cell types, a group collectively known as 'eukaryotes'. This observation has puzzled scientists for decades: How could the complex cell types from eukaryotes have emerged from the simple cells of Archaea?

In this weeks' edition of Nature, researchers from Uppsala University in Sweden, along with collaborators from the universities in Bergen (Norway) and Vienna (Austria) report the discovery of a new group of Archaea, the Lokiarchaeota (or 'Loki' for short), and identify it to be a missing link in the origin of eukaryotes.

"The puzzle of the origin of the eukaryotic cell is extremely complicated, as many pieces are still missing. We hoped that Loki would reveal a few more pieces of the puzzle, but when we obtained the first results, we couldn't believe our eyes. The data simply looked spectacular", says Thijs Ettema at the Department of Cell and Molecular Biology, Uppsala University, who lead the scientific team that carried out the study.

"By studying its genome, we found that Loki represents an intermediate form in-between the simple cells of microbes, and the complex cell types of eukaryotes", says Thijs Ettema.

When Loki was placed in the Tree of Life, this idea was confirmed.

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Major Clades of Archaea Originated by Pursuing Bacteria Down Alleyways to Beat Them Unconscious and Riffle Their Genetic Pockets

Origins of major archaeal clades correspond to gene acquisitions from bacteria

Authors:

Nelson-Sathi et al

Abstract:

The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms—ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions. To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxa.

Last Universal Common Ancestor of all Life on Earth had a Leaky Membrane, Lived in Deep Sea Vents

All life on Earth came from one common ancestor – a single-celled organism – but what it looked like, how it lived and how it evolved into today's modern cells is a four billion year old mystery being solved by researchers at UCL using mathematical modelling.

Findings published today in PLOS Biology suggest for the first time that life's Last Universal Common Ancestor (LUCA) had a 'leaky' membrane, which helps scientists answer two of biology's biggest questions:

1. Why all cells use the same bizarre, complex mechanism to harvest energy

2. Why two types of single-celled organism that form the deepest branch on the tree of life – bacteria and archaea – have completely different cell membranes

The leakiness of the membrane allowed LUCA to be powered by energy in its surroundings, most likely vents deep on the ocean floor, whilst holding in all the other components necessary for life.

The team modelled how the membrane changed, enabling LUCA's descendants to move to new, more challenging environments and evolve into two distinct types of single-celled organism, bacteria and archaea, creating the deepest branch of the tree of life.

Bacteria and archaea share many common features such as genes, proteins and mechanisms of reading DNA, initially leading scientists to believe they were just different types of bacteria. Their classification changed in the 1970's after extreme differences were found in the way they replicate DNA and in the structure of their cell membrane. As they both stemmed from LUCA, scientists set out to find answers in the structure and function of LUCA's membrane.

Dr Nick Lane (UCL Biosciences) who led the study said, "I find this work just beautiful – it constrains a sequence of steps going from the strange cell that seems to have been the ancestor of all life today, right through to the deep division between modern cells. From a single basic idea, the model can explain the fundamental differences between bacteria and archaea. Is it right? I'd like to think so, but more importantly, it makes some clear predictions that we plan to test in the future."

Data from the study strongly suggest that LUCA lived in the area where ancient seawater, dense with positively charged particles called protons, mixed with warm alkaline vent fluid, which contained few protons. The difference in the concentration of protons across these two environments enabled protons to flow into the cell, driving the production of a molecule called adenosine triphosphate (ATP) which powered the growth of cells, just as it does today. However, unlike modern cells the scientists believe this could only happen if the membrane was 'leaky', enabling protons to leave the cell spontaneously so more protons could enter to power growth.

Dr Lane said: "In these deep sea vents, there is a continuous flow of alkaline fluids, which mix with the ocean waters. When they mix, the fluids neutralise each other, and that stops any build-up of charge which would otherwise prevent protons flowing into the cell. If the first cells had leaky membranes, then protons could enter and then be neutralised, or leave again, almost as if there was no barrier at all. What we've shown is that the rate at which protons enter and leave is high enough to power the growth of cells via proteins embedded in the membrane. So LUCA could have been powered by natural proton gradients in vents, but only if it had a really leaky membrane, completely unlike today's cells."

To escape from these seabed vents, LUCA had to adapt its membrane to pump protons out of the cell, in order for them to flow back in again to help drive ATP production. The study suggests that the bacteria and archaea developed completely different cell membrane structures and proton pumps, whilst keeping the same machinery for powering growth. It also explains why they differ in fundamental traits that depend on the membrane such as DNA replication.

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A Potential Carbon Source for Subsurface, Martian Methanogenic Life

Potential Use of Highly Insoluble Carbonates as Carbon Sources by Methanogens in the Subsurface of Mars

Authors:

Kral et al

Abstract:

Methanogens, microorganisms in the domain Archaea, have been studied as life forms that might inhabit the subsurface of Mars. These organisms can use carbon dioxide as a carbon source, a compound that is abundant in the martian atmosphere. But if they exist in the deep subsurface where the carbon dioxide may not penetrate, they would have to rely on another source of carbon. Magnesium carbonate and calcium carbonate have been detected at the martian surface, and there is no reason to believe that they would not be in the subsurface as well. In the research reported here, we asked if these carbonates could possibly serve as carbon sources for four species of methanogens. Methanothermobacter wolfeii, Methanobacterium formicicum and Methanococcus maripaludis were able to produce a small amount of methane (approximately 0.4–0.8% headspace gas) when either carbonate was the carbon source available while Methanosarcina barkeri only produced significant methane (also 0.4–0.8%) when calcium carbonate was the carbon source. The amounts produced were dependent on methanogenic species, carbonate used and pH. At equilibrium, a small amount of carbon dioxide (approximately 0.05–0.15% headspace gas as well as in liquid media) was generated by these carbonates, and this carbon dioxide was most likely the carbon compound that was being metabolized. Background carbon dioxide from the atmosphere was not sufficient for measureable methane production.

Evidence of a Black Smoker Biota From PaleoArchean Australia?

Geochemistry and nano-structure of a putative ∼3,240 million-year-old black smoker biota, Sulfur Springs Group, Western Australia

Authors:

Wacey et al

Abstract:

Filaments of pyrite found within a volcanic hosted massive sulfide (VHMS) deposit from the ∼3,270-3,230 Ma Sulfur Springs Group of Western Australia have previously been interpreted as remnants of some of Earth's oldest thermophilic microbial communities. We here re-examine these pyrite filaments using a suite of in situ high spatial resolution techniques and provide new observations on their geochemistry, morphology, texture, distribution and habitat.

A number of the Sulfur Springs filaments retain geochemical evidence for remnants of organic material. This takes the form of patches of carbon and nitrogen enrichment seemingly enclosed within a completely pyritised filament. The distribution of this organic material closely resembles that observed in younger bona fide pyritised filamentous microbes. Most filaments also possess a distinctive sponge-like nano-porous pyrite texture, which is replicated in younger pyritised microfossils and bio-mediated pyrite framboids, and is consistent with pyrite nucleation in an organic matrix. New 3D analyses confirm previous observations of approximately uniform filament diameters, lack of branching, clustering of filaments, plus zones of filaments with preferred orientations. Multiple sulfur isotope analyses indicate that the sulfur for pyritisation likely came from a mixture of seawater and magmatic sources, consistent with a black smoker type habitat and permissive of the presence of life in this setting.

While these data are consistent with a biological interpretation for the Sulfur Springs filaments, perhaps as pyritised filamentous microorganisms or bundles of pyritised extra-cellular polymeric substances (EPS), the evidence is not compelling. Solid filament cross-sections and straight lengthwise morphology of most filaments resemble abiotic crystal needles or whiskers, while the parallel and radial alignments of filaments could be replicated by crystal growth patterns. Carbon and nitrogen enrichment could have occurred when organic material entrained within hydrothermal fluids was adsorbed onto these mineral crystals. Further work to obtain larger databases of nano-scale textures and morphologies from both biological and abiotic pyrite is needed before an abiotic formation mechanism can be confidently rejected.

Methanosarcina Developed Efficient Methanogenic Pathways at the Time of the Permian Extinction

Methanogenic burst in the end-Permian carbon cycle

Authors:

Rothman et al

Abstract:

The end-Permian extinction is associated with a mysterious disruption to Earth’s carbon cycle. Here we identify causal mechanisms via three observations. First, we show that geochemical signals indicate superexponential growth of the marine inorganic carbon reservoir, coincident with the extinction and consistent with the expansion of a new microbial metabolic pathway. Second, we show that the efficient acetoclastic pathway in Methanosarcina emerged at a time statistically indistinguishable from the extinction. Finally, we show that nickel concentrations in South China sediments increased sharply at the extinction, probably as a consequence of massive Siberian volcanism, enabling a methanogenic expansion by removal of nickel limitation. Collectively, these results are consistent with the instigation of Earth’s greatest mass extinction by a specific microbial innovation.

Hints the Last Universal Common Ancestor for Bacteria and Archaea was Cold Adapted

The molecular signal for the adaptation to cold temperature during early life on Earth

Authors:

Groussin et al

Abstract:

Several lines of evidence such as the basal location of thermophilic lineages in large-scale phylogenetic trees and the ancestral sequence reconstruction of single enzymes or large protein concatenations support the conclusion that the ancestors of the bacterial and archaeal domains were thermophilic organisms which were adapted to hot environments during the early stages of the Earth. A parsimonious reasoning would therefore suggest that the last universal common ancestor (LUCA) was also thermophilic. Various authors have used branch-wise non-homogeneous evolutionary models that better capture the variation of molecular compositions among lineages to accurately reconstruct the ancestral G + C contents of ribosomal RNAs and the ancestral amino acid composition of highly conserved proteins. They confirmed the thermophilic nature of the ancestors of Bacteria and Archaea but concluded that LUCA, their last common ancestor, was a mesophilic organism having a moderate optimal growth temperature. In this letter, we investigate the unknown nature of the phylogenetic signal that informs ancestral sequence reconstruction to support this non-parsimonious scenario. We find that rate variation across sites of molecular sequences provides information at different time scales by recording the oldest adaptation to temperature in slow-evolving regions and subsequent adaptations in fast-evolving ones.

I missed this the first time for some reason.

New Subsurface Mars Compatible Microbe Found from Siberian Permafrost

Single-cell analysis of the methanogenic archaeon Methanosarcina soligelidi from Siberian permafrost by means of confocal Raman microspectrocopy for astrobiological research

Authors:

Serrano et al

Abstract:

Methanogenic archaea from Siberian permafrost are suitable model organisms that meet many of the preconditions for survival on the martian subsurface. These microorganisms have proven to be highly resistant when exposed to diverse stress factors such as desiccation, radiation and other thermo-physical martian conditions. In addition, the metabolic requirements of methanogenic archaea are in principle compatible with the environmental conditions of the Red Planet.

The ExoMars mission will deploy a rover carrying a Raman spectrometer among the analytical instruments in order to search for signatures of life and to investigate the martian geochemistry. Raman spectroscopy is known as a powerful nondestructive optical technique for biosignature detection that requires only little sample preparation. In this study, we describe the use of confocal Raman microspectroscopy (CRM) as a rapid and sensitive technique for characterization of the methanogenic archaeon Methanosarcina soligelidi SMA-21 at the single cell level. These studies involved acquisition of Raman spectra from individual cells isolated from microbial cultures at different stages of growth. Spectral analyses indicated a high degree of heterogeneity between cells of individual cultures and also demonstrated the existence of growth-phase specific Raman patterns. For example, besides common Raman patterns of microbial cells, CRM additionally revealed the presence of lipid vesicles and CaCO3 particles in microbial preparations of M. soligelidi SMA-21, a finding that could be confirmed by electron microscopy. The results of this study suggest that heterogeneity and diversity of microorganisms have to be considered when using Raman-based technologies in future space exploration missions.

Salt Loving Extremophiles Inhabit Antarctica's Deep Lake

A team led by scientists at the University of New South Wales has uncovered the genetic secrets of "extremophile" microbes that can survive in water temperatures as low as minus 20 degrees in the saltiest lake in Antarctica.

Deep Lake, about five kilometres from Davis Station, was formed about 3500 years ago, when the Antarctic continent rose, isolating a section of ocean. The water in the 36-metre deep lake is now so salty it remains in liquid form down to a temperature of minus 20 degrees.

"The lake has the distinction of being the least productive lake ever recorded, with very little able to grow in it," says Professor Rick Cavicchioli, of the UNSW School of Biotechnology and Biomolecular Sciences, and leader of the team.

The team took water samples from the lake at depths of five, 13, 24 and 36 metres, and studied the entire genetic sequence, or genome, of the microbes living there, to work out how they had evolved to cope with the extremely harsh conditions.

The results are published in the journal Proceedings of the National Academy of Sciences.

The extremophiles present belong to a group of microbes - haloarchaea – that are known to be "promiscuous", swapping DNA between themselves.

"But our research shows these ones swap much more genetic material with each other than has been observed in the natural environment before. Long stretches of virtually identical DNA are exchanged between different genera, not just species," says Professor Cavicchioli.

"Despite this rampant gene swapping, the different species are maintained and can co-exist because they have evolved to exploit different niches and consume different food sources."

Some, for example, consume proteins in the water; others consume sugars like glycerol, from algae living on the lake surface. It is estimated the haloarchaea grow very slowly in the lake, with only about six generations produced a year.

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"Wolfe, these things aren’t even bacteria!" A Exposition on Archaea

Carl Woese died Dec. 30. Woese remains little known, even among non-microbial biologists but particularly among the public. He endured a decade or more of skepticism, ridicule, and ostracism before his observations were accepted and was deeply hurt by the initial reaction [...] In recent years, some — including the editorial board at Nature Reviews Microbiology — pushed for Woese to receive the Nobel prize for his contributions. Now, that will never happen.

But Woese is not the only unsung hero in this story. The organisms he revealed — the archaea — are fascinating and abundant creatures, yet are hardly ever discussed in depth, even within the confines of microbiology classes. That is a shame. Archaea are everywhere — in deep sea vents, in salt flats, in ice, in sea water, in soil, and in you. And they deserve better publicity.

Go. Read. They Are AWESOME.