Tag: Bacteria

Photosynthesis, arsenic and a window on the Archaean world

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At the very base of the biological pyramid life is far simpler than that which we can see.  It takes the form of single cells that lack a nucleus and propagate only by cloning: the prokaryotes as opposed to eukaryote life such as ourselves. It is almost certain that the first viable life on Earth was prokaryotic, though which of its two fundamental divisions – Archaea or Bacteria – came first is still debated. At present, most prokaryotes metabolise other organisms’ waste or dead remains: they are heterotrophs (from the Greek for ‘other nutrition’). But there are others that are primary producers getting their nutrition by themselves, exploiting the inorganic world in a variety of ways: the autotrophs. Biogeochemical evidence from the earliest sedimentary rocks suggests that, in the Archaean prokaryotic autotrophs were dominant, mainly exploiting chemical reactions to gain energy necessary for building carbohydrates. Some reduced sulfate ions to those of sulphide, others combined hydrogen with carbon dioxide to generate methane as a by-product. Sunlight being an abundant energy resource in near-surface water, a whole range of prokaryotes exploit its potential through photosynthesis. Under reducing conditions some photosynthesisers convert sulfur to sulfuric acid , yet others combine photosynthesis with chemo-autotrophy. Dissolved material capable of donating electrons – i.e. reducing agents – are exploited in photosynthesis: hydrogen, ferrous iron (Fe2+), reduced sulfur, nitrite, or some organic molecules. Without one group, which uses photosynthesis to convert CO2 and water to carbohydrates and oxygen, eukaryotes would never have arisen, for they depend on free oxygen. A transformation 2400 Ma ago marked a point in Earth history when oxygen first entered the atmosphere and shallow water (see: Massive event in the Precambrian carbon cycle; January, 2012), known as Great Oxygenation Event (GOE). It has been shown that the most likely sources of that excess oxygen were extensive bacterial mats in shallow water made of photosynthesising blue-green bacteria that produced the distinctive carbonate structures known as stromatolites. These had formed in Archaean sedimentary basins for 1.9 billion years. It has been generally assumed that blue-green bacteria had formed them too, before the oxygen that they produced overcame the reducing conditions that had generally prevailed before the GOE. But that may not have been the case …

Microbial mats made by purple sulfur bacteria in highly toxic spring water flowing into a salt-lake in northern Chile. (credit: Visscher et al. 2020; Fig 1c)

Prokaryotes are a versatile group and new types keep turning up as researchers explore all kinds of strange and extreme environments, for instance: hot springs; groundwater from kilometres below the surface and highly toxic waters. A recent surprise arose from the study of anoxic springs laden with dissolved salts, sulfide ions and arsenic that feed parts of hypersaline lakes in northern Chile (Visscher, P.T. and 14 others 2020. Modern arsenotrophic microbial mats provide an analogue for life in the anoxic Archean. Communications Earth & Environment, v. 1, article 24; DOI: 10.1038/s43247-020-00025-2). This is a decidedly extreme environment for life, as we know it, made more challenging by its high altitude exposure to high UV radiation. The springs’ beds are covered with bright-purple microbial mats. Interestingly the water’s arsenic concentration varies from high in winter to low in summer, suggesting that some process removes it, along with sulfur, according to light levels: almost certainly the growth and dormancy of mat-forming bacteria. Arsenic is an electron donor capable of participating in photosynthesis that doesn’t produce oxygen. The microbial mats do produce no oxygen whatever – uniquely for the modern Earth – but they do form carbonate crusts that look like stromatolites. The mats contain purple sulfur bacteria (PSBs) that are anaerobic photosynthesisers, which use sulfur, hydrogen and Fe2+ as electron donors. The seasonal changes in arsenic concentration match similar shifts in sulfur, suggesting that arsenic is also being used by the PSBs. Indeed they can, as the aio gene, which encodes for such an eventuality, is present in the genome of PSBs.

Pieter Visscher and his multinational co-authors argue for prokaryotes similar to modern PSBs having played a role in creating the stromatolites found in Archaean sedimentary rocks. Oxygen-poor, the Archaean atmosphere would have contained no ozone so that high-energy UV would have bathed the Earth’s surface and its oceans to a considerable depth. Moreover, arsenic is today removed from most surface water by adsorption on iron hydroxides, a product of modern oxidising conditions (see: Arsenic hazard on a global scale; May 2020): it would have been more abundant before the GOE. So the Atacama springs may be an appropriate micro-analogue for Archaean conditions, a hypothesis that the authors address with reference to the geochemistry of sedimentary rocks in Western Australia deposited in a late-Archaean evaporating lake. Stromatolites in the Tumbiana Formation show, according to the authors, definite evidence for sulfur and arsenic cycling similar to that in that Atacama springs. They also suggest that photosynthesising blue-green bacteria (cyanobacteria) may not have viable under such Archaean conditions while microbes with similar metabolism to PSBs probably were. The eventual appearance and rise of oxygen once cyanobacteria did evolve, perhaps in the late-Archaean, left PSBs and most other anaerobic microbes, to which oxygen spells death, as a minority faction trapped in what are became ‘extreme’ environments when long before they ‘ruled the roost’. It raises the question, ‘What if cyanobacteria had not evolved?’. A trite answer would be, ‘I would not be writing this and nor would you be reading it!’. But it is a question that can be properly applied to the issue of alien life beyond Earth, perhaps on Mars. Currently, attempts are being made to detect oxygen in the atmospheres of exoplanets orbiting other stars, as a ‘sure sign’ that life evolved and thrived there too. That may be a fruitless venture, because life happily thrived during Earth’s Archaean Eon until its closing episodes without producing a whiff of oxygen.

See also: Living in an anoxic world: Microbes using arsenic are a link to early life. (Science Daily, 22 September 2020)

‘Mud, mud, glorious mud’

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Earth is a water world, which is one reason why we are here. But when it comes to sedimentary rocks, mud is Number 1. Earth’s oceans and seas hide vast amounts of mud that have accumulated on their floors since Pangaea began to split apart about 200 Ma ago during the Early Jurassic. Half the sedimentary record on the continents since 4 billion years ago is made of mudstones. They are the ultimate products of the weathering of crystalline igneous rocks, whose main minerals – feldspars, pyroxenes, amphiboles, olivines and micas, with the exception of quartz – are all prone to breakdown by the action of the weakly acidic properties of rainwater and the CO2 dissolved in it. Aside from more resistant quartz grains, the main solid products of weathering are clay minerals (hydrated aluminosilicates) and iron oxides and hydroxides. Except for silicon, aluminium and ferric iron, most metals end up in solution and ultimately the oceans.  As well as being a natural product of weathering, mud is today generated by several large industries, and humans have been dabbling in natural muds since the invention of pottery some 25 thousand years ago.  On 21 August 2020 the journal Science devoted 18 pages to a Special Issue on mud, with seven reviews (Malakoff, D. 2020. Mud. Science, v. 369, p. 894-895; DOI: 10.1126/science.369.6506.894).

Mud carnival in Brazil (Credit: africanews.com)

The rate at which mud accumulates as sediment depends on the rate at which erosion takes place, as well as on weathering. Once arable farming had spread widely, deforestation and tilling the soil sparked an increase in soil erosion and therefore in the transportation and deposition of muddy sediment. The spurt becomes noticeable in the sedimentary record of river deltas, such as that of the Nile, about 5000 years ago. But human influences have also had negative effects, particularly through dams. Harnessing stream flow to power mills and forges generally required dams and leats. During medieval times water power exploded in Europe and has since spread exponentially through every continent except Antarctica, with a similar growth in the capacity of reservoirs. As well as damming drainage these efforts also capture mud and other sediments. A study of drainage basins in north-east USA, along which mill dams quickly spread following European colonisation in the 17th century, revealed their major effects on valley geomorphology and hydrology (see: Watermills and meanders; March 2008). Up to 5 metres of sediment build-up changed stream flow to an extent that this now almost vanished industry has stoked-up the chances of major flooding downstream and a host of other environmental changes. The authors of the study are acknowledged in one Mud article (Voosen, P. 2020. A muddy legacy. Science, v. 369, p. 898-901; DOI: 10.1126/science.369.6506.898) because they have since demonstrated that the effects in Pennsylania are reversible if the ‘legacy’ sediment is removed. The same cannot be expected for truly vast reservoirs once they eventually fill with muds to become useless. While big dams continue to function, alluvium downstream is being starved of fresh mud that over millennia made it highly and continuously productive for arable farming, as in the case of Egypt, the lower Colorado River delta and the lower Yangtze flood plain below China’s Three Gorges Dam.

Mud poses extreme risk when set in motion. Unlike sand, clay deposits saturated with water are thixotropic – when static they appear solid and stable but as soon as they begin to move en masse they behave as a viscous fluid. Once mudflows slow they solidify again, burying and trapping whatever and whomever they have carried off. This is a major threat from the storage of industrially created muds in tailings ponds, exemplified by a disaster at a Brazilian mine in 2019, first at the site itself and then as the mud entered a river system and eventually reached the sea. Warren Cornwall explains how these failures happen and may be prevented (Cornwall, W. 2020. A dam big problem.  Science, v. 369, p. 906-909; DOI: 10.1126/science.369.6506.906). Another article in the Mud special issue considers waste from aluminium plants (Service, R.F. 2020. Red alert. Science, v. 369, p. 910-911; DOI: 10.1126/science.369.6506.910). The main ore for aluminium is bauxite, which is the product of extreme chemical weathering in the tropics. The metal is smelted from aluminium hydroxides formed when silica is leached out of clay minerals, but this has to be separated from clay minerals and iron oxides that form a high proportion of commercial bauxites, and which are disposed of in tailings dams. The retaining dam of such a waste pond in Hungary gave way in 2010, the thixotropic red clay burying a town downstream to kill 10 people. This mud was highly alkaline and inflicted severe burns on 150 survivors. Service also points out a more positive aspect of clay-rich mud: it can absorb CO2 bubbled through it to form various, non-toxic carbonates and help draw down the greenhouse gas.

Muddy sediments are chemically complex, partly because their very low permeability hinders oxygenated water from entering them: they maintain highly reducing conditions. Because of this, oxidising bacteria are excluded, so that much of the organic matter deposited in the muds remains as carbonaceous particles. They store carbon extracted from the atmosphere by surface plankton whose remains sink to the ocean floor. Consequently, many mudrocks are potential source rocks for petroleum. Although they do not support oxygen-demanding animals, they are colonised by bacteria of many different kinds. Some – methanogens – break down organic molecules to produce methane. The metabolism of others depends on sulfate ions in the trapped water, which they reduce to sulfide ions and thus hydrogen sulfide gas: most muds stink. Some of the H2S reacts with metal ions, to precipitate sulfide minerals, the most common being pyrite (FeS2). In fact a significant proportion of the world’s copper, zinc and lead resources reside in sulfide-rich mudstones: essential to the economies of Zambia and the Democratic Republic of Congo. But there are some strange features of mud-loving bacteria that are only just emerging. The latest is the discovery of bacteria that build chains up to 5 cm long that conduct electricity (Pennisi, E. 2020. The mud is electric. Science, v. 369, p. 902-905; DOI: 10.1126/science.369.6506.902). The bacterial ‘nanowires’ sprout from minute pyrite grains, and transfer electrons released by oxidation of organic compounds, effectively to catalyse sulfide-producing reduction reactions. NB Oxygen is not necessary for oxidation as its chemistry involves the loss of electrons, while reduction involves a gain of electrons, expressed by the acronym OILRIG (oxidation is loss, reduction is gain). It seems such electrical bacteria are part of a hitherto unsuspected chemical ecosystem that helps hold the mud together as well as participating in a host of geochemical cycles. They may spur an entirely new field of nano-technology, extending, bizarrely, to an ability to generate electricity from moisture in the air.

If you wish to read these reviews in full, you might try using their DOIs at Sci Hub.