Science | giant bacteria found in mangroves challenge the traditional concept of nuclear free membrane

subject ：A centimeter-long bacterium with DNA contained in metabolically active membrane-bound organelles

DOI：https://doi.org/10.1126/science.abb3634

Date of publication ：2022-06-23

First author ：Jean-Marie Volland, Silvina Gonzalez-Rizzo, Olivier Gros

Corresponding author ：Tanja Woyke, Shailesh V. Date

Communication unit ：Department of Energy Joint Genome Institute

Reading guide

microorganism , seeing the name of a thing one thinks of its function , That is, an organism that cannot be directly observed by the naked eye in our traditional concept , It is necessary to assist the microscope and other tools to capture the physiological morphology and other information . So far, , The known bacterial volume is usually 0.4∼3 µm Between , But in the latest issue Science in ,Volland Et al 、X X-ray and electron microscopy combined with genome sequencing , It represents a kind of visible “ Centimeter scale ” Sulfur oxidizing bacteria —— Gram negative Proteus Thiomargarita magnifica, It was found on the deposited leaves of mangroves in the sulfur-containing waters of the Guadeloupe Islands , And the average cell length is greater than 9000 micron . The size of these cells in bacteria exceeds the growth limit of traditional theory by several orders of magnitude , Showing an unprecedented level of surpassing 50 Polyploidy of a very large genome with 10000 copies , And experienced a two-state life cycle of asymmetric chromosome separation to daughter cells . These findings challenge the traditional concept of bacterial cells , And help to study the factors that limit cell size .

Artistically presents Ca. Thiomargarita magnifica And coins .( source ： Mangrove photos ,Pierre Yves Pascal; illustrations ,Susan Brand/ Berkeley Lab ) – By Massie S. Ballon

At first glance , The slightly muddy water in the test tube looks like a spoonful of rain , Among them are leaves 、 Debris , There are even lighter threads . But in a Petri dish , As thin as silk thread, it floats gently on the leaf litter , This is a single bacterial cell visible to the naked eye .

This unusual size is amazing , Because bacteria are usually difficult to observe without the help of a microscope ." It's bigger than most bacteria 5,000 times .”Jean-Marie Volland say , He is the US Department of energy （DOE） Joint Genomics Institute （JGI） A scientist of . This year, 6 month 24 The latest issue of 《Science》 The magazine reported Volland And colleagues' research , In this paper, the morphological and genomic characteristics of the giant filamentous bacteria are described in detail , And its life cycle .

Ca.Thiomargarita magnifica A single flagellum  ( source : Jean-Marie Volland)

For most bacteria , Their DNA Floating freely in the cytoplasm , And the newly discovered bacteria DNA More organized . The biggest surprise of the project was that we found that these genome copies spread throughout the cell were actually contained in a membrane structure ,"Volland say ," And this is unique for a bacterium ."

A strange encounter in the mangroves

The bacterium was originally developed by Professor of marine biology at the University of Antilles in Guadeloupe Olivier Groz stay 2009 Discovered in 2003 .Groz The focus of the study is the marine mangrove system , When he first observed the bacteria , Looking for sulfur oxide symbionts in sulfur rich mangrove sediments not far from his laboratory ." He said ：" When I see them , I'm surprised , At first I thought it was just some strange white filaments , It needs to be attached to the leaves and other surfaces in the sediment ." In the next few years, the laboratory carried out more systematic microscopic research on them , And realize that this is a sulfur oxidizing prokaryote .

The co-author of the study was an associate professor of molecular biology at the University of Antilles Silvina Gonzalez-Rizzo, She did 16S rRNA After sequencing, it was identified as a prokaryote ." Due to the large volume of these microorganisms and the filamentous form they present , I thought they were eukaryotes at first , Not bacteria  ", She recalled that ," We realize that they are very unique , Because it looks like a single cell , They are a kind of ' Macroscopic ' Of microbes " .Gonz It is found that this is a kind of Thiomargarita Bacteria of the genus , And name it Ca. Thiomargarita magnifica.

"Magnifica Because magnus It means big in Latin , I think it's like a French word magnifique As gorgeous ,"Gonzalez-Rizzo explains ." This discovery opens the door to a new world of bacterial forms that have never been studied before ".

Identify the characteristics of giant bacteria

When Volland As a postdoctoral researcher, I returned to Groz In the laboratory , He was involved in a huge Thiomargarita The study of bacteria . When he applied in LRC The position of , Will be in JGI Work ,Groz Allow him to continue his research on the project .

Volland stay Tanja Woyke The single-cell research group began to study Ca. T. magnifica, To better understand this sulfur oxide 、 The role of carbon fixing bacteria in mangroves ." Mangrove and its microbiome are important ecosystems of carbon cycle . If you look at the space they occupy on a global scale , It is less than... In the coastal areas of the world 1%. But when you look at carbon storage , You will find that they contribute to the 10-15% Our carbon ,"Woyke say , He is also JGI The head of the microbiology project , Is one of the authors of the article . Given the potential interactions between these large bacteria and other microorganisms , The team also conducted research ."Woyke say ：" We are JGI Start this project under the strategic theme of interactions between organisms , Because large sulfur bacteria have been proved to be the hot spot of symbiosis ." She added ：" However , This project takes us in a very different direction .

View of sampling points in mangrove forests of Guadeloupe .( source : Olivier Groz)

Volland Accepted the challenge , Three dimensional visualization of cells at high magnification . Using various microscope techniques , Such as X X-ray tomography , He saw long 9.66 mm A complete filament of , And confirmed that they are indeed huge single cells , Not multicellular filaments , This is common in other large sulfur bacteria . He was also able to take advantage of the existing imaging facilities at Berkeley laboratories , Such as confocal laser scanning microscope and transmission electron microscope （TEM）, Observe filaments and cell membranes in more detail . These techniques enabled him to observe the presence of DNA The new of the cluster 、 Membrane bound chambers . He called these organelles  "pepins", Named after the small seeds in the fruit .DNA Clusters are very numerous in single cells .

The team learned about the genomic complexity of cells . just as Volland Pointed out ," These bacteria contain three times more genes than most bacteria , And hundreds of thousands of copies of the genome throughout the cell （ polyploid ）".JGI The team then used single-cell genomics to analyze five bacterial cells at the molecular level . They amplified, sequenced and assembled the genome . meanwhile ,Groz The lab also uses a BONCAT To identify the sites involved in active protein translation , This confirms that the entire bacterial cell is active .

"LRC Founder and CEO of Shailesh Date Is one of the authors of the article , He said ：" This project is a good opportunity , Can demonstrate how complexity evolves in some of the simplest organisms ." One of the things we have demonstrated is , It is necessary to observe and study biological complexity in more detail . therefore , We think very simple organisms may also have some surprises ."

The law research center passed John - Templeton Foundation and Gordon and Betty - The Moore Foundation funded walland ." Gordon and Betty - Moore Foundation Sara Bender Add ：" This groundbreaking discovery underscores the support for foundational 、 The importance of creative research projects , To promote our understanding of nature ." We look forward to learning Ca. Thiomargarita magnifica How do the characteristics of challenge the current patterns that make up bacterial cells , And promote microbial research .”

From the left .Tanja Woyke, Jean-Marie Volland, Olivier Groz, Silvina Gonzalez-Rizzo and  Shailesh Date.( source : Hugo Bret, Susan Brand/ Berkeley Lab )

A huge bacterium , Multiple research questions

For the team , describe Ca. Thiomargarita magnifica Characteristics of , It paves the way for many new research problems . among , The role of this bacterium in mangrove ecosystems .Volland say ：" We know it grows and thrives on the sediments of the mangrove ecosystem in the Caribbean ,"." In metabolism , It is chemically synthesized , This is a process similar to plant photosynthesis ." Another outstanding issue is , Was named pepins Whether the new organelles are in Thiomargarita magnifica Played a role in the evolution of extreme size , as well as pepins Whether it exists in other bacterial species .pepins The precise formation of these structures and how these internal and external molecular processes occur and are regulated remain to be studied .

Gonzalez-Rizzo and Woyke It is believed that the successful cultivation of these bacteria in the laboratory is the way to get the answer .”Woyke say ：" If we can maintain these bacteria in a laboratory environment , We can use more technology . Gross wants to see other large bacteria ." You can find some TEM Pictures of the , See something like a saber , But I don't know what they are . If the saber has been everywhere , This will be a very interesting exploration ".

From the National Museum of natural history （ The French ）、 Sorbonne University （ The French ） And researchers from Cornell University are also involved in this work .

Organization Profile

The joint Genomics Institute of the U. S. Department of energy is located at the Lawrence Berkeley National Laboratory , Committed to advancing genomics , To support DOE's tasks related to clean energy production and environmental characterization and clean-up .JGI Provides comprehensive high-throughput sequencing and computational analysis , Enable systems based scientific approaches to address these challenges .

Lawrence Berkeley National Laboratory was established in 1931 year , The idea is that the biggest scientific challenge should be solved by the team , The laboratory and its scientists have obtained 14 A Nobel Prize . today , Berkeley Lab researchers develop sustainable energy and environmental solutions , Create useful new materials , Advancing the frontiers of computing , And explore life 、 The mysteries of matter and the universe . Scientists around the world rely on laboratory facilities for their own research . Berkeley Laboratory is a multi project national laboratory , Managed by the University of California for the U.S. Department of energy science office .

The science office of the Department of energy is the largest supporter of basic research in Physical Science in the United States , And is working to address some of the most pressing challenges of our time .

The original report ：https://newscenter.lbl.gov/2022/06/23/giant-bacteria-found-in-guadeloupe-mangroves-challenge-traditional-concepts/

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