Abstract
AU Consortia: Pleaseconfirmthatallheadinglevelsarerepresentedcorrectly of multicellular magnetotactic bacteria (MMB) are:currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.
| Original language | English |
|---|---|
| Article number | e3002638 |
| Journal | PLoS Biology |
| Volume | 22 |
| Issue number | 7 July |
| DOIs | |
| State | Published - Jul 2024 |
| Externally published | Yes |
Funding
This study was funded through NASA Exobiology program award NNX17AK85G to R.H. and NASA FINESST award 80NSSC20K1365 to G. S. and R.H. A portion of this research was performed under the Community Sciences Program (awards DOI: 10.46936/10.25585/ 60001107 and DOI: 10.46936/10.25585/ 60001212) and used resources at the DOE Joint Genome Institute (https://ror.org/04xm1d337), which is a DOE Office of Science User Facility operated under Contract No. DE-AC02-05CH11231. A portion of this research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program under awards DOI: 10.46936/fics.proj.2017.49972/ 6000002 to R.H. and 10.46936/fics.proj.2020. 51544/60000211 to R.H. and used resources at the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), which is a DOE Office of Science User Facilities operated under Contract No. DE-AC05-76RL01830. Fluorescence and Raman microscopy imaging was made possible by The Center for Biofilm Engineering Imaging Facility at Montana State University, which is supported by funding from the NSF MRI Program (2018562), the M. J. Murdock Charitable Trust (202016116), the US Department of Defense (77369LSRIP), and by the Montana Nanotechnology Facility (an NNCI member supported by NSF Grant ECCS-2025391). Montana State University\u2019s Confocal Raman microscope was acquired with support by the National Science Foundation (DBI-1726561) and the M. J. Murdock Charitable Trust (SR-2017331). The National Institute of General Medical Sciences (P30GM140963) provided support to C.G. The Simons Foundation (824763) provided support to S.E.R. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank Jeffrey Marlow (Boston University), Rachel Spietz (MSU), and Ashley Cohen (MSU) for help with the collection of LSSM sediment samples and assistance with lab work as well as Heidi Smith (MSU) for microscopy support. We also thank Anthony Kohtz, Amanda Wilkins, and Hope McWilliams (all MSU) for assistance with lab work, Marike Palmer (University of Nevada Las Vegas) for discussions on taxonomy, Julie Huber (Woods Hole Oceanographic Institution) for graciously providing access to her lab space at WHOI, and Kristina Hillesland (University of Washington, Bothell) for critical comments that helped to improve the manuscript. We thank our Brazilian colleagues Fernanda Abreu, Henrique Lins de Barros, Marcos Farina, Carolina Keim, and Juliana Martins (Lopez), as well as Sherri Simmons for their foundational work on MMB and allowing us to name newly discovered MMB species after them and in honor of the late Ulysses Lins, who transformed our understanding of MMB.