November 2024
·
92 Reads
·
1 Citation
Cell Reports
This page lists works of an author who doesn't have a ResearchGate profile or hasn't added the works to their profile yet. It is automatically generated from public (personal) data to further our legitimate goal of comprehensive and accurate scientific recordkeeping. If you are this author and want this page removed, please let us know.
November 2024
·
92 Reads
·
1 Citation
Cell Reports
August 2024
·
86 Reads
·
1 Citation
Background Magnetotactic bacteria (MTB) are a unique group of microorganisms that sense and navigate through the geomagnetic field by biomineralizing magnetic nanoparticles. MTB from the phylum Nitrospirota (previously known as Nitrospirae) thrive in diverse aquatic ecosystems. They are of great interest due to their production of hundreds of magnetite (Fe3O4) magnetosome nanoparticles per cell, which far exceeds that of other MTB. The morphological, phylogenetic, and genomic diversity of Nitrospirota MTB have been extensively studied. However, the metabolism and ecophysiology of Nitrospirota MTB are largely unknown due to the lack of cultivation techniques. Methods Here, we established a method to link the morphological, genomic, and metabolic investigations of an uncultured Nitrospirota MTB population (named LHC-1) at the single-cell level using nanoscale secondary-ion mass spectrometry (NanoSIMS) in combination with rRNA-based in situ hybridization and target-specific mini-metagenomics. Results We magnetically separated LHC-1 from a freshwater lake and reconstructed the draft genome of LHC-1 using genome-resolved mini-metagenomics. We found that 10 LHC-1 cells were sufficient as a template to obtain a high-quality draft genome. Genomic analysis revealed that LHC-1 has the potential for CO2 fixation and NO3⁻ reduction, which was further characterized at the single-cell level by combining stable-isotope incubations and NanoSIMS analyses over time. Additionally, the NanoSIMS results revealed specific element distributions in LHC-1, and that the heterogeneity of CO2 and NO3⁻ metabolisms among different LHC-1 cells increased with incubation time. Conclusions To our knowledge, this study provides the first metabolic measurements of individual Nitrospirota MTB cells to decipher their ecophysiological traits. The procedure constructed in this study provides a promising strategy to simultaneously investigate the morphology, genome, and ecophysiology of uncultured microbes in natural environments. 6gfJ7qtcG81szcFZGMmDYdVideo Abstract
April 2024
·
130 Reads
·
1 Citation
Magnetotactic bacteria (MTB) capable of magnetosome organelle biomineralization and magnetotaxis are widespread in chemically stratified aquatic environments. Conventionally, it has long been considered that the overall abundance of MTB in microbiota is not very high and that Magnetococcia is the most frequently identified and predominant MTB members. However, the diversity and distribution of MTB in chemically stratified environments remain elusive due to the lack of large-scale systematic analyses. Here we conduct a comprehensive survey of genomes containing magnetosome gene clusters (MGCs), a group of genes responsible for magnetosome biomineralization and magnetotaxis, in 267 metagenomes from 38 oxygen-stratified freshwater environments. A total of 63 MGC-containing genomes belonging to eight bacterial phyla are reconstructed, including the newly identified Myxococcota. We discover an unexpectedly high relative abundance of putative MTB (up to 15.4% of metagenomic reads) in hypoxic and anoxic water columns, in which Deltaproteobacteria, rather than traditionally considered Magnetococcia, are the most ubiquitous and predominant MGC-containing bacteria. Our analysis reveals a depth-specific taxonomy and function of MGC-containing bacteria in stratified water columns shaped by physicochemical conditions. These findings underscore the unrecognized ecophysiological importance of MTB in freshwater ecosystems.
January 2022
·
120 Reads
·
9 Citations
Microbiology Resource Announcements
Magnetosome gene clusters (MGCs), which are responsible for magnetosome biosynthesis and organization in magnetotactic bacteria (MTB), are the key to deciphering the mechanisms and evolutionary origin of magnetoreception, organelle biogenesis, and intracellular biomineralization in bacteria. Here, we report the development of MagCluster, a Python stand-alone tool for efficient exploration of MGCs from large-scale (meta)genomic data.
August 2020
·
149 Reads
·
5 Citations
Microbiology Resource Announcements
Magnetotactic bacteria represent a valuable model system for the study of microbial biomineralization and magnetotaxis. Here, we report two metagenome-assembled genome sequences of uncultivated magnetotactic bacteria belonging to the order Magnetococcales . These genomes contain nearly complete magnetosome gene clusters responsible for magnetosome biomineralization.
... 8,[37][38][39][40][41] Together, the widespread distribution and high abundance of MTB emphasize their remarkable adaptability and their crucial ecological roles, such as geochemical cycling of C, N, and Fe. 42,43 How magnetosomes contribute to MTB survival in different extreme environments is an interesting avenue for future research. ...
August 2024
... 27,35 Recent large-scale metagenomic investigations indicate that the relative abundance of MTB within the hypoxic and anoxic freshwater area can be quite high (up to 15.4% of metagenomic reads). 36 Deltaproteobacteria, rather than the traditionally considered Magnetococcia (Candidatus Etaproteobacteria), have been identified as the most ubiquitous and predominant MGC-containing bacteria in freshwater columns. 36 Furthermore, MTB can thrive in extreme aquatic environments, including extreme temperatures, pH, salinity, and pressure. ...
April 2024
... 32 Overall, MTB have been discovered across at least 17 bacterial phyla (Figure 1), highlighting their remarkable phylogenetic diversity. Recently, several standalone tools, such as FeGenie 33 and MagCluster, 34 have been developed to efficiently explore MGCs from large-scale (meta) genomic datasets, further facilitating the discovery of new MTB species. ...
January 2022
Microbiology Resource Announcements
... To obtain sufficient DNA for metagenomic sequencing, whole-genome amplification was carried out using the multiple displacement amplification technique with the Genomiphi V2 DNA Amplification Kit (GE Healthcare, United States). This approach has been widely used previously in various works (Kolinko et al., 2015;Monteil et al., 2019;Zhang et al., 2020b). The amplified DNA was purified by sodium acetate precipitation. ...
August 2020
Microbiology Resource Announcements