Identification and Genomic Characterization of Two Previously Unknown Magnetotactic Nitrospirae

Zhang, Wensi; Wang, Yinzhao; Liu, Li; Pan, Yongxin; Lin, Wei

doi:10.3389/fmicb.2021.690052

Cited by 9 publications

(27 citation statements)

References 73 publications

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“…Consistent with previous studies, all of the magnetotactic representatives appear to have the ability for autotrophy using Wood-Ljungdahl and heterotrophy by glycolysis via Embden-Meyerhof pathways [56,62]. In addition, all Nitrospirota MTB are potentially capable of dissimilatory sulfur oxidation.…”

Section: Discussionsupporting

confidence: 87%

“…Comparative analysis showed common traits for Nitrospirota MTB. MGC of all genomes, with some exceptions, consisted of three separate clusters that were highly conservative, which was also noted by Zhang et al [56]. No principal differences were found in metabolic features between the magnetotactic Nitrospirota genomes.…”

Section: Discussionsupporting

confidence: 80%

“…The other two clades include single genomes of Ca . Magnetomicrobium cryptolimnococcus XYC and nDJH13bin3, respectively [56]. Two Nitrospirota genomes, nDJH8bin7 and nDJH14bin9, belong to a separate family.…”

Section: Resultsmentioning

confidence: 99%

“…Unfortunately, there is no available pure culture of Nitrospirota MTB, making it difficult to accurately characterize their physiology, ecology, and magnetosome formation process. All known magnetotactic Nitrospirota were studied using culture-independent techniques [62,67,68,[70][71][72][73][74], and the morphology of many Nitrospirota MTB is known through the FISH-TEM approaches [56,68,70,73]. In this study, two novel Nitrospirota genomes were reconstructed, which expanded MTB's genomic diversity.…”

Section: Discussionmentioning

confidence: 99%

“…Ca. Magnetobacterium cryptolimnobacter XYR [56]. Besides, there is a difference in MGC composition between representatives of Ca.…”

Section: Magnetomonas Plexicatena Lbb01 Previously the Duplication Of...mentioning

confidence: 99%

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Detection of interphylum transfers of the magnetosome gene cluster in magnetotactic bacteria

Uzun

Koziaeva

Dziuba

et al. 2022

Preprint

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Magnetosome synthesis in magnetotactic bacteria (MTB) is regarded as a very ancient evolutionary process that dates back to deep-branching phyla. MTB belonging to one of such phyla, Nitrospirota, contain the classical genes for the magnetosome synthesis (e.g., mam, mms) and man genes, which were considered to be specific for this group. However, the recent discovery of man genes in MTB from the Thermodesulfobacteriota phylum has raised several questions about the inheritance of these genes in MTB. In this work, three new man genes containing MTB genomes affiliated with Nitrospirota and Thermodesulfobacteriota, were obtained. By applying reconciliation with these and the previously published MTB genomes, we demonstrate that the last common ancestor of all Nitrospirota was most likely not magnetotactic as assumed previously. Instead, our findings suggest that the genes for magnetosome synthesis were transmitted to the phylum Nitrospirota by horizontal gene transfer (HGT), which is the first case of the interphylum transfer of magnetosome genes detected to date. Furthermore, we provide evidence for the HGT of magnetosome genes from the Magnetobacteriaceae to the Dissulfurispiraceae family within Nitrospirota. Thus, our results imply a more significant role of HGT in the MTB evolution than deemed before and challenge the hypothesis of the ancient origin of magnetosome synthesis.

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Section: Discussionsupporting

confidence: 87%

Section: Discussionsupporting

confidence: 80%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…Ca. Magnetobacterium cryptolimnobacter XYR [56]. Besides, there is a difference in MGC composition between representatives of Ca.…”

Section: Magnetomonas Plexicatena Lbb01 Previously the Duplication Of...mentioning

confidence: 99%

See 3 more Smart Citations

Detection of interphylum transfers of the magnetosome gene cluster in magnetotactic bacteria

Uzun

Koziaeva

Dziuba

et al. 2022

Preprint

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Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota

et al. 2023

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The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms important to biogeochemical and industrial processes. These phyla are common inhabitants of marine and terrestrial subsurface environments and contain members capable of diverse physiologies in addition to nitrite oxidation and complete ammonia oxidation. Here, we use phylogenomics and gene-based analysis with ancestral state reconstruction and gene-tree–species-tree reconciliation methods to investigate the life histories of these two phyla. We find that basal clades of both phyla primarily inhabit marine and terrestrial subsurface environments. The genomes of basal clades in both phyla appear smaller and more densely coded than the later-branching clades. The extant basal clades of both phyla share many traits inferred to be present in their respective common ancestors, including hydrogen, one-carbon, and sulfur-based metabolisms. Later-branching groups, namely the more frequently studied classes Nitrospiria and Nitrospinia, are both characterized by genome expansions driven by either de novo origination or laterally transferred genes that encode functions expanding their metabolic repertoire. These expansions include gene clusters that perform the unique nitrogen metabolisms that both phyla are most well known for. Our analyses support replicated evolutionary histories of these two bacterial phyla, with modern subsurface environments representing a genomic repository for the coding potential of ancestral metabolic traits.

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Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications

Goswami

et al. 2022

npj Biofilms Microbiomes

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Magnetotactic bacteria (MTB) are a group of phylogenetically diverse and morphologically varied microorganisms with a magnetoresponsive capability called magnetotaxis or microbial magnetoreception. MTB are a distinctive constituent of the microbiome of aquatic ecosystems because they use Earth’s magnetic field to align themselves in a north or south facing direction and efficiently navigate to their favored microenvironments. They have been identified worldwide from diverse aquatic and waterlogged microbiomes, including freshwater, saline, brackish and marine ecosystems, and some extreme environments. MTB play important roles in the biogeochemical cycling of iron, sulphur, phosphorus, carbon and nitrogen in nature and have been recognized from in vitro cultures to sequester heavy metals like selenium, cadmium, and tellurium, which makes them prospective candidate organisms for aquatic pollution bioremediation. The role of MTB in environmental systems is not limited to their lifespan; after death, fossil magnetosomal magnetic nanoparticles (known as magnetofossils) are a promising proxy for recording paleoenvironmental change and geomagnetic field history. Here, we summarize the ecology, evolution, and environmental function of MTB and the paleoenvironmental implications of magnetofossils in light of recent discoveries.

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Identification and Genomic Characterization of Two Previously Unknown Magnetotactic Nitrospirae

Cited by 9 publications

References 73 publications

Detection of interphylum transfers of the magnetosome gene cluster in magnetotactic bacteria

Detection of interphylum transfers of the magnetosome gene cluster in magnetotactic bacteria

Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota

Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications

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