New publication looking at the biodiversity and ecology of globally distributed bacteria

Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups

Deltaproteobacteria, now proposed to be the phyla Desulfobacterota, Myxococcota, and SAR324, are ubiquitous in marine environments and play essential roles in global carbon, sulfur, and nutrient cycling. Despite their importance, our understanding of these bacteria is biased towards cultured organisms. Here we address this gap by compiling a genomic catalog of 1 792 genomes, including 402 newly reconstructed and characterized metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments. Phylogenomic analyses reveal that many of these novel MAGs are uncultured representatives of Myxococcota and Desulfobacterota that are understudied. To better characterize Deltaproteobacteria diversity, metabolism, and ecology, we clustered ~1 500 genomes based on the presence/absence patterns of their protein families. Protein content analysis coupled with large-scale metabolic reconstructions separates eight genomic clusters of Deltaproteobacteria with unique metabolic profiles. While these eight clusters largely correspond to phylogeny, there are exceptions where more distantly related organisms appear to have similar ecological roles and closely related organisms have distinct protein content. Our analyses have identified previously unrecognized roles in the cycling of methylamines and denitrification among uncultured Deltaproteobacteria. This new view of Deltaproteobacteria diversity expands our understanding of these dominant bacteria and highlights metabolic abilities across diverse taxa.

The start of it all (from The Texas Scientist magazine)

Dinosaurs, daisies, starfish and humans are all made up of cells containing tiny biological hitchhikers. In all complex life, each cell has an energy-producing organelle that has its own DNA and looks and acts suspiciously like bacteria. In animals, they’re called mitochondria; in plants, they’re called chloroplasts.

How they got there is an open question and one researchers like Brett Baker, a faculty member in The University of Texas at Austin Department of Marine Science, explore. Baker thinks the answer may go something like this:

  • About 2 billion years ago, a microbe called an archaeon gobbled up a free-floating bacterium, and it worked well for both parties. The bacterium provided new energy sources to the archaeon, which in turn provided safety and nutrients.

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Early Archaeon

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Bacterium
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Archaeon gobbling up bacteria
  • Over time the two previously free-living microbes spawned a single, hybrid offspring — the first eukaryote.

  • All complex, multicellular life on the planet evolved from this new lifeform.

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Eukaryote with mitochondria

Baker and his colleagues have uncovered evidence that a recently discovered group of microbes, called the Asgard archaea, were the original hosts to give rise to all eukaryotes, including us humans. With support from the Moore-Simons Project, the scientists are now investigating which Asgards are most closely related to eukaryotes and further exploring their physiological interactions and cellular structure.

Brockarchaeota, a new archaeal phylum with unique and versatile pathways for carbon cycling

With some sadness, I announce the publication of new Archaea recovered from hot springs around the world. Named Brockarchaeota in honor of microbio pioneer Thomas Brock. Tom recently passed away, but told me he was honored. rdcu.be/cjeBh

Climate-friendly Microbes Chomp Dead Plants Without Releasing Heat-trapping Methane

UT press release.

Baker lab leading a new project to understand the origin of eukaryotes funded by the Simons and Moore Foundations

New Initiative Aims to Reveal the Origins of Complex Life

A new research initiative will shed light on how the origin of complex life evolved through symbiosis. The project will be the latest from the Brett Baker laboratory at The University of Texas at Austin’s Marine Science Institute, which made recent discoveries of new organisms called Asgard archaea, named after Norse gods, and their metabolisms.

The Asgards are commonly found at the bottom of the ocean near hydrothermal vents, and these discoveries brought scientists closer to understanding how more complex life, known as eukaryotes, came to be. The MooreSimons Project on the Origin of the Eukaryotic Cell has awarded a grant to Baker and his colleagues (Dr. Thijs Ettema Wageningen at University in the Netherlands, Dr. Mark Ellisman at University of California San Diego, and Dr. Roland Hatzenpichler at Montana State University) to prove or disprove ideas about the origin of complex life.

There is currently a fundamental gap in the understanding of the origin of eukaryotes (including plants and animals). The leading theory is that eukaryotes, with their complex cells full of organelles encased in a cellular membrane, evolved when one simple organism absorbed another, its bacterial symbiont. The recently discovered Asgard archaea are the closest relatives of eukaryotes known and are a descendant of the host of this relationship that led to the first eukaryotic cells. Studies of these Asgard microbes are revolutionizing our understanding of the origin of eukaryotic life.

There are several competing hypotheses on the biological and physiological interactions that led to the symbiotic origin of eukaryotes, and the newly funded research will advance our understanding of this relationship. Scientists know that the evolution of mitochondria material was a pivotal point in eukaryotic evolution because these organelles have their own DNA and are important powerhouses of the eukaryotic cell, creating most of the chemical energy. Recent evidence collected by this team indicate that this absorption may have first occurred in an Asgard host microbe when it took over a bacteria – that has the genes and proteins to produce energy.

The new initiative, supported with nearly $2 million from the Moore-Simons Project on the Origin of the Eukaryotic Cell, will allow Baker and colleagues to determine which Asgards are most closely related to eukaryotes and further explore their physiological interactions, and cellular structure.

“Our research will transform our understanding of the microbial interactions that led to the formation of eukaryotic life on the planet,” says Baker.

 

New review in press at Annual Review in Marine Science

New microbial biodiversity in marine sediments

Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling.