Previously undescribed lineage of Archaea illuminates microbial
evolution

Date:
August 10, 2020
Source:
Royal Netherlands Institute for Sea Research
Summary:
Scientists describe a previously unknown phylum of aquatic Archaea
that are likely dependent on partner organisms for growth while
potentially being able to conserve some energy by fermentation.



FULL STORY ==========================================================================
In a publication in Nature Communications last Friday, NIOZ scientists
Nina Dombrowski and Anja Spang and their collaboration partners describe a previously unknown phylum of aquatic Archaea that are likely dependent on partner organisms for growth while potentially being able to conserve some energy by fermentation. In contrast to initial analyses, this study shows
that the new phylum is part of a group of Archaea that are believed to
mainly comprise symbionts. Further, the study yields new insights into
the diversity and evolutionary history of the Archaea.


========================================================================== Archaea make up one of the main divisions of life, next to the Bacteria
and the Eukaryotes, the latter of which comprise for example fungi,
plants and animals.

Archaea are a large group of microorganisms that live in all habitats
on Earth ranging from soils and sediments to marine and freshwater
environments as well as from human-made to host-associated habitats
including the gut. In turn, Archaea are now thought to play a major role
in biogeochemical nutrient cycles.

In a publication in Nature Communications last Friday, evolutionary microbiologists Nina Dombrowski and Anja Spang from the Royal Netherlands Institute of Sea Research (NIOZ) describe a previously unknown archaeal
lineage (phylum). The authors named them the Undinarchaeota, in reference
to the female water spirit or nymph Undina. For the study, Dombrowski and
Spang cooperated with partners from Bristol University, the University
of Queensland and the Australian National University.

Diverse symbionts and parasites Because of their great resemblance to
Bacteria, Archaea were only described as a separate lineage about 40
years ago and were not studied intensely until very recently, when it
became possible to sequence DNA directly from environmental samples
and to reconstruct genomes from uncultivated organisms. This field of
genetic research, generally referred to as metagenomics, has not only
revealed that microbial life including the Archaea is much more diverse
than originally thought, but also provided data needed to shed light on
the function of these microbes in their environments.

The newly described Undinarchaeota were discovered in genetic material
from marine (Indian, Mediterranean and Atlantic ocean) and aquifer (Rifle aquiver, Colorado River) environments. The authors could show that they
belong to a very diverse and until recently unknown group of so-called
DPANN archaea. Members of the DPANN include organisms with very small
genomes and limited metabolic capabilities, which suggests that these
organisms depend on other microbes for growth and survival1,2,3. In
fact, the few so far cultivated DPANN archaea are obligate symbionts or parasites that cannot live on their own4.



==========================================================================
"In line with this, the Undinarchaeota seem to lack several anabolic
pathways, indicating that they are, too, depend on various metabolites
from so far unknown partner organisms," says research leader Anja
Spang. "However, Undinarchaeota seem to have certain metabolic pathways
that lack in some of the most parasitic DPANN archaea and may be able
to conserve energy by fermentation." Complex evolutionary history While
DPANN have only been discovered recently, it becomes increasingly clear
that they are widespread and that representatives inhabit all thinkable environments on Earth. Yet, little is known about their evolutionary and ecological role. "In some way, some of the DPANN archaea resemble viruses, needing a host organism, likely other archaea or bacteria, for survival,"
says Spang. "However, and in contrast to viruses, we currently know
very little about the DPANN archaea and how they affect food webs and
host evolution. It is also unclear whether DPANN are an ancient archaeal lineage that resembles early cellular life or have evolved later or in
parallel with their hosts." With their study, the authors could shed more light on the complex evolution of Archaea. "Our work revealed that many
DPANN archaea frequently exchange genes with their hosts, which makes
it very challenging to reconstruct their evolutionary history," says
first author Nina Dombrowski. Tom Williams (Bristol University) adds:
"However, we could show that DPANN have probably evolved in parallel
with their hosts over a long evolutionary time scale, by identifying
and studying those genes that were inherited from parent-to-offspring
instead of having been transferred between host and symbiont." Role in
marine biogeochemical cycles Spang expects that certain DPANN including
the Undinarchaeota, may be important for biogeochemical nutrient cycles
within the oceans and sediments. "One reason that DPANN were discovered relatively recently, is that they were not retained on the filters
originally used for concentrating cells from environmental samples due to
their small cell sizes." But since their discovery, DPANN turned out to
be much more widespread than originally anticipated. Chris Rinke from the University of Queensland: "Prospective research on the Undinarchaeota and
other DPANN archaea will be essential to obtain a better understanding
of marine biogeochemical cycles and the role symbionts play in the transformation of organic matter." These questions drive some of the prospective projects of Anja Spang. In particular, in collaboration with
their NIOZ colleagues Laura Villanueva, Pierre Offre and Julia Engelmann,
the authors of the publication Anja Spang and Nina Dombrowski have just sequenced new DNA from water samples from the Black Sea, revealing that Undinarchaeota are present in almost all anoxic depth layers of this
basin. Spang says: "These data are a gold mine for the future exploration
of the ecology and evolution of these potentially symbiotic Archaea,
allowing us to identify their interaction partners and to unravel further secrets about the biology of the Undinarchaeota."

========================================================================== Story Source: Materials provided by Royal_Netherlands_Institute_for_Sea_Research. Note: Content may be edited
for style and length.


========================================================================== Journal Reference:
1. Nina Dombrowski, Tom A. Williams, Jiarui Sun, Benjamin J. Woodcroft,
Jun-
Hoe Lee, Bui Quang Minh, Christian Rinke, Anja Spang. Undinarchaeota
illuminate DPANN phylogeny and the impact of gene transfer on
archaeal evolution. Nature Communications, 2020; 11 (1) DOI:
10.1038/s41467-020- 17408-w ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/08/200810103322.htm

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