Nanobactérias hiperativas com hospedeiro

Nature Microbiology volume 8, páginas 727–744 (2023)Cite este artigo

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O filo bacteriano candidato Omnitrophota não foi isolado e é pouco compreendido. Analisamos 72 genomas de Omnitrophota recém-sequenciados e 349 existentes, representando 6 classes e 276 espécies, juntamente com dados do Projeto Microbioma da Terra para avaliar habitat, características metabólicas e estilos de vida. Aplicamos triagem de células ativadas por fluorescência e filtração de tamanho diferencial, e mostramos que a maioria dos Omnitrophota são células ultrapequenas (~ 0,2 μm) encontradas em água, sedimentos e solos. Os genomas de Omnitrophota em 6 classes são reduzidos, mas mantêm as principais vias biossintéticas e de conservação de energia, incluindo acetogênese (com ou sem a via Wood-Ljungdahl) e respirações diversas. Pelo menos 64% dos genomas de Omnitrophota codificam agrupamentos de genes típicos de simbiontes bacterianos, sugerindo estilos de vida associados ao hospedeiro. Nós reaproveitamos dados quantitativos de sondagem de isótopos estáveis de solos dominados por intemperismo de andesito, basalto ou granito e identificamos 3 famílias com alta absorção de isótopos consistentes com predadores bacterianos obrigatórios. Propomos que a maioria dos Omnitrophota habite vários ecossistemas como predadores ou parasitas.

O filo bacteriano candidato Omnitrophota (sinônimos: OP3, Omnitrophya, Omnitrophyaeota; aqui formalmente denominado Omnitrophota) foi identificado em pesquisas do gene RNA ribossômico 16S , particularmente em água e sedimentos. Estudos publicados sobre o gene 16S rRNA e baseados em metagenoma colocaram Omnitrophota no superfilo Planctomycetota – Verrucomicrobiota – Chlamydiota (PVC). Omnitrophota não foi isolada e apenas duas espécies foram observadas microscopicamente. 'Candidatus Omnitrophus magneticus' SKK-01 (ref. 5) foi descrita como uma bactéria magnética grande, ovóide, supostamente de vida livre, contendo inclusões de enxofre (aqui referida como SKK-01). 'Cá. O LiM6 de Velamenicoccus archaeovorus foi identificado como um coco pequeno (0,2–0,3 μm) presente em culturas de enriquecimento metanogênicas e degradadoras de limoneno, tanto como células livres quanto como epibionte de outras bactérias ou arquéias, incluindo Methanosaeta6. Ao viver como epibionte, V. archaeovorus tem uma produção transcricional diferente, aumenta o conteúdo do ribossomo e parece danificar ou matar as células hospedeiras6. Dados os diferentes estilos de vida de SKK-01 e V. archaeovorus LiM, não está claro se algum deles é um representante significativo para o filo.

Relatórios anteriores propuseram que as capacidades metabólicas dos genomas amplificados únicos (SAGs) de Omnitrophota e dos genomas montados por metagenoma (MAGs) incluem respiração aeróbica heterotrófica ou acetogênese . A genômica comparativa de 14 MAGs Omnitrophota de um lago antártico e um único MAG de sedimentos do Mar Negro sugeriu que todos eram fermentadores obrigatórios . Até agora, no entanto, tem faltado um esforço sistemático para interpretar os dados genómicos no contexto do filo Omnitrophota.

Aqui analisamos um compêndio de SAGs (75) e MAGs (346), juntamente com estudos de tamanho celular e metabolismo in situ para apresentar um quadro mais abrangente da biologia de Omnitropphota.

Os genomas (421) classificados como Omnitrophota foram coletados a partir de nossos próprios dados novos (72 genomas) e dados existentes (349 genomas), incluindo 75 SAGs e 346 MAGs (Fig. 1 e Tabela Suplementar 1). Os genomas originaram-se de amostras de biomas ambientais, incluindo águas de lagos ou rios (111), águas subterrâneas (97), sedimentos geotérmicos (64), solos a granel (59), águas residuais (37) e sedimentos marinhos ou salinos (30).

a, Estimativas do tamanho do genoma para ≥90% dos genomas Omnitrophota completos. b, Estatísticas de integridade do genoma e detecção do gene 16S rRNA de todos os genomas de Omnitrophota incluídos nesta análise. As cores representam classes. Em aeb, os boxplots representam intervalos interquartis, as barras horizontais/verticais são médias e as barras verticais/horizontais são intervalos de confiança de 95%. c, Filogenia de máxima verossimilhança construída a partir do conjunto concatenado de marcadores Bac120 de 204 representantes de espécies de Omnitrophota. O número entre parênteses no final de cada ponta corresponde ao ID do genoma na Tabela Suplementar 1. Os nós pontilhados indicam suporte SH-aLRT ≥80% e suporte UFboot ≥95%.

70% of EMP samples. Soils displayed the highest taxonomic specificity, with only Omnitrophia, Velamenicoccia and class 2-02-FULL-51-18 occurring at high frequencies. Omnitrophia, Velamenicoccia and Gorgyraia occurred at higher relative abundances in anoxic aquatic environments relative to oxic waters. We propose a broad physicochemical niche for Omnitrophota, with most members being part of the rare biosphere./p>0.3 μm. On the basis of several marker gene sets, we concluded that the SAGs were not contaminated (Extended Data Fig. 1, and Supplementary Figs. 1 and 2), suggesting that either single cells were >0.3 μm or they might be dividing or are single-species aggregates. MAGs (112) from serially filtered cells revealed some species small enough to pass through a 0.2 μm filter in the Velamenicoccia (3), Gorgyraia (3) and Omnitrophia (2) classes (Fig. 2a). Similar to the SAGs, only a few MAGs were recovered from larger size fractions (>0.65 μm) from across the phylum, including Velamenicoccia (5 MAGs), Gorgyraia (8 MAGs), Omnitrophia (3 MAGs), Aquiviventia (1 MAG) and class 2-02-FULL-51-18 (1 MAG); however, whether these represent single cells >0.65 μm or aggregates is unclear. We note that 16S rRNA gene amplicon sequencing of abundant Omnitrophota populations from serial-filtered source water from Cave Spring, Kiup Spring and Grapevine Springs, all in the Spring Mountains of Nevada, produced similar results: all five classes and 13/14 families were more abundant on 0.2 μm filters than on 0.45 μm filters in all springs following tandem filtration (Fig. 2b,c). Together, these results show that cells of all classes of Omnitrophota are frequently among the smallest known cells (Supplementary Table 4)./p>0.5 μm, filled large circle). ‘Acetogen/WLP’, Wood-Ljungdahl pathway and acetogenesis; ‘acs2’, acetyl-CoA synthetase; ‘acsABCDE’, CO dehydrogenase/acetyl-CoA synthase; ‘Respiration’, ‘e- acceptors’ and ‘H2ase’ (hydrogenase) indicate genes predicted to encode proteins involved in energy metabolism. ‘Lo-O2’, cytochrome c oxidase complex; ‘Hi-O2’, cytochrome bd ubiquinol; ‘M+’, metal-reducing cytochromes; ‘e- Pilin’, conductive pili. Symbiosis-related genes include ‘T4aP’ (type-4a pilus), ‘Tad’ (tight-adherence pilus), ‘sF-ATP (‘symbiotic’ type 2/3 FoF1 ATPase α-subunit), ‘Translocase’ (ATP/ADP translocase) and ‘big ORF’ (indicating the presence of a large ORF). ‘Temp’, ‘O2’ and ‘pH’ indicate the observed temperature, oxygen concentration (mM) and pH of the sample from which each genome was sequenced. Data for additional Omnitrophota genomes are summarized in Supplementary Fig. 10./p>75% of 204 high- and medium-quality species representative genomes encoded biosynthetic pathways for nucleotides, all 20 amino acids, NAD, glutathione, pantothenate, coenzyme A, riboflavin, tetrahydrofolate and thiamine. Biosynthetic pathways for heme, cobalamin and biotin were present but not universal (that is, <75% of genomes). Biosynthetic pathways for pyridoxal-5P (M00124) were missing or incomplete across the phylum. C5-isoprenoid biosynthesis (M00096) was complete or near-complete and 4-hydroxybenzoate polyprenyltransferase was detected in >50% of genomes of the Omnitrophia and Aquiviventia, satisfying the requirements to commit 4-hydroxybenzoate to ubiquinone biosynthesis via 4-hydroxy-3-polyprenylbenzoate (M00017). However, chorismate-pyruvate lyase was not detected, so ubiquinone biosynthesis may initiate from an alternate source of 4-hydroxybenzoate rather than chorismate. Menaquinone biosynthetic pathways (M00016) were present in some Velamenicoccia genomes, particularly Zapsychrales. Quinone biosynthesis genes were absent from genomes of 2-02-FULL-51-18 species. Compared with other species from the PVC superphylum, genes not mapping to COGs were reduced in both richness and percentage (P < 0.05, one-way ANOVA and post-hoc Tukey’s HSD) (Supplementary Fig. 6). These analyses show that this phylum has a propensity towards small, streamlined genomes that retain most genes essential for a free-living lifestyle, including energy conservation./p>1% and <50% of species, or deleted if present in only one or no species. See Supplementary Tables 5 and 6 for details of these features for ANI cluster representatives. Red X indicates enzyme/complex is absent in Omnitrophota. * indicates canonical ubiquinone pathway is not complete./p>0.65 μm; Fig. 2). However, serial filtration and FACS indicated both large and small cell sizes in the class, and the scattering of systems indicating possible symbiosis suggests a complex history for this class./p> 0.05, ANOVA with post-hoc Tukey’s HSD) but were higher than those of facultative predators such as Lysobacter, Myxococcales and Streptomycetaceae, and free-living bacteria en masse (P < 0.05, ANOVA with post-hoc Tukey’s HSD; Supplementary Fig. 16); thus, we describe them as hyperactive. We caution against the interpretation that these Omnitrophota are necessarily obligate predators because their small cell size, and therefore higher DNA/biomass stoichiometry, might contribute to higher 18O content of Omnitrophota and other small cells. However, high isotope incorporation of facultative predators with large cell size in the same datasets and in other soils48 argues that the overall isotope incorporation pattern observed here for Omnitrophota is due to some form of symbiosis. Family 2-02-FULL-51-18 also assimilated high amounts of 13C-labelled glucose and oxalate, although long incubation times and high soil community complexity complicate interpretation of carbon source utilization./p>2.5 kbp using MetaBAT2 (ref. 55). The estimated quality of binned MAGs was evaluated using CheckM56, and initial classification was done using the GTDB Toolkit16 v1.1.010 to identify MAGs belonging to Omnitrophota./p>4 members. Additionally, some phyla, such as Firmicutes (labelled Firmicutes_A, Firmicutes_B and so on in GTDB) were collapsed into single units for simplicity. All phylum pairs and Omnitrophota class/phylum pairs were compared using ANOVA followed by Tukey’s HSD. The quantile of each Omnitrophota genome was then calculated as a function of this genome collection./p>

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