Brazilian researchers have reconstructed the evolutionary history of amoeba and showed that at the end of the Precambrian period, at least 750 million years ago, life on Earth was far more diverse than suggested by classical theory.
The study, supported by the São Paulo Research Foundation – FAPESP, revealed eight new ancestral lineages of Thecamoebae, the largest group in Amoebozoa. Thecamoebian is known as the testis because of its hard outer carapace or shell.
The interpretation of the evolution of the Earth's atmosphere and climate change is also influenced by the discovery that amoeba is more diverse than previously thought.
In this study, published in the journal Current Biology, researchers affiliated with the University of São Paulo Bioscience Institute (IB-USP) in Brazil, in partnership with colleagues at Mississippi State University in the United States, use innovative techniques to reconstruct the Thecamoeba phylogenetic (evolutionary) tree that belongs Arcellinida command.
The new phylogenetic tree was created using mathematical and transcriptomic algorithms from 19 arcellinids found in nature today. The researchers also determined the morphology and composition of this hypothetical ancestor of the amoeba group and compared it with the fossil record.
The results showed that at least 750 million years ago, the ancestors of husband and wife had evolved. This finding shows that the late Prambambrian was more diverse than previously thought.
"We reach our conclusions using a combination of two major scientific fields – paleontology and phylogenetic systematics, fields in biology that reconstruct evolutionary history and study patterns of relationships between organisms. In this way, we can decipher one of the vertices in the theory of evolution on life on this planet, "said Daniel Lahr, a professor at IB-USP and the lead author of the article.
The researchers fully dismantled the previous classification of the farmers. "We managed to develop a strong structure and for the first time, found eight deep lineages [from 750 million years ago] about arcellinids which is unknown, "Lahr said.
The oldamoamo classification is based on the composition of the shell. "They are divided into aglutinates and organics. However, from our molecular reconstruction, we find that the actual classification is determined by the shape of the shell rather than composition," said Lahr.
The old classification, he continued, has been questioned for several years, but more evidence is needed to destroy it. Previous genetic research has shown that the classification is not sustainable, but not enough data is available to justify the new classification.
"The scientific community suspects that amelin arcellinid testates have emerged and evolved adequately to diversify around 750 million years ago. We have now succeeded in showing this hypothesis," he said.
Past and future
According to Lahr, this study presents a different view of how microorganisms evolved on the planet. Late Precambrian is considered a period of low biotic diversity, with only a few species of bacteria and some protists.
"In this period 800 million years ago the oceans became oxygenated. For a long time, oxygenation was assumed to have caused diversification of eukaryotes, unicellular and multicellular organisms where cell nuclei were isolated by membranes, culminating in diversification of macroorganisms millions of years later in the Cambrian," Lahr said .
The study published in Current Biology, he added, focuses on the details of this question. "We show that diversification seems to have existed in the precambrian and may occur together with ocean oxygenation. What's more, geophysicists find that this process is slow and may have lasted around 100 million years or more," he said.
However, scientists do not know what pressure triggers this oxygenation. "Regardless of the cause, oxygenation eventually causes more niches, diversified eukaryotes, and there is more competition for niches. One way to resolve competition is that some lineages become larger and therefore multicellular," Lahr said.
This study also contributes to a better understanding of current climate change. "We are beginning to understand more deeply how these microbial lives affect the planet in a number of ways," Lahr said. "The climate changed fundamentally during that period, which saw the occurrence of the Sturtian glacial around 717 million years ago. This is one of the biggest glacial events that has ever existed."
According to Lahr, this change might have a biological origin. "By increasing the resolution of how life evolved in a very remote past, we can understand a little better how life affects the planet's climate and even its geology. That will help us understand the climate change we are experiencing right now," he said.
On the rock
In addition to the discovery of greater diversity in the Precambrian, this study also innovated by reconstructing the morphology of ancestors of farmers to establish that vase-shaped microfossils (VSM) found in various parts of the world already existed in the Precambrian and even in the major ice ages that occurred during this era .
VSM is considered an amoeba testate fossil. They are unicellular and eukaryotic and have an external framework. The significant diversity of VSM has been documented for the Neoproterozoic Era, which stretched between 1 billion and 541 million years ago, and is the last era of the precambrian.
"This study is a very different vision of how microorganisms evolve on this planet. Although fossils do not contain genetic information, it is possible to obtain morphological information and composition and to verify whether they are organic or silica-based. So, it is possible to compare their chemical form and composition, which in this case is well preserved, with people from scientists now being reshaped by big data, "said Luana Morais, a postdoctoral researcher with a scholarship from FAPESP and co-author of the article.
In addition to the lack of fossils containing DNA, the researchers faced another obstacle in reconstructing the phylogenetic tree: the farmers could not be cultured in the laboratory, and therefore genetic sequencing in the conventional way was ruled out.
The solution to this problem is to use a single cell transcriptom technique to analyze phylogenetics (instead of gene expression, its normal application). "We sequence all transcriptomes from arcellinid urea using direct samples," explained Lahr. "This produces several thousand genes and around 100,000 amino acid sites, or 100,000 data points giving us phylogenetic trees, which have never been seen before."
The researchers used a transcriptome-based methodology to capture all messenger RNA from each individual cell and turn it into a sequential complementary DNA library.
"Our research fundamentally uses single cell transcriptom, where our lab is one of the pioneers around the world," Lahr said. "This is a revolutionary technique in this field because it allows us to find one [unicellular] amoeba, isolate and clean it, and do all laboratory procedures to sort the entire transcriptome. "
In this study, the researchers chose 250 genes to build phylogenetic trees. "It's no use just looking at one cell when you study gene expression, because resolution won't be enough," Lahr said. "However, in an evolutionary study, this is not a problem. You need to get the sequence, not the number of times a gene is expressed. So it is possible to use this technique, which was originally developed for tumor cells, and adapt it, with the advantage that amoeba cells are far bigger than tumor cells. "
Before techniques are developed, only organisms that grow in the laboratory can be sorted. "This broadens the scope of my research in this field by allowing me to get genetic information from organisms that I only found once. It is estimated that only 1% or less of all biodiversity can be cultivated," Lahr said.