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Phylogenetic position of Vampirovibrio chlorellavorus in the phylum Cyanobacteria. (A) A maximum likelihood (ML) phylogenetic tree of the phylum Cyanobacteria inferred from a concatenated alignment of 109 single copy marker genes conserved across the bacterial domain. Black circles represent branch nodes with >90% bootstrap support by ML analysis. Class Oxyphotobacteria group names are according to Shih et al. (2013). The blue and red arrow indicate putative acquisition and loss of flagella respectively in the class Melainabacteria. Representatives of 32 bacterial phyla were used as outgroups in the analysis (Fig. S2). Ca, Candidatus. (B) A ML tree of the order Vampirovibrionales (Soo et al., 2014) based on aligned 16S rRNA gene sequences from the May, 2013 Greengenes database (McDonald et al., 2012). Black circles represent nodes with >90% ML, maximum parsimony (MP) and neighbour joining (NJ) bootstrap support values.
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An uncultured non-photosynthetic basal lineage of the Cyanobacteria, the Melainabacteria, was recently characterised by metagenomic analyses of aphotic environmental samples. However, a predatory bacterium, Vampirovibrio chlorella-vorus, originally described in 1972 appears to be the first cultured representative of the Melainabacteria based on a 1...
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... (https://github.com/hadley/ggplot2) was used to plot GC content against coverage allowing contigs belonging to the V. chlorellavorus genome to be identified. A discrete cluster of contigs with >180× coverage and a GC range of 42-54% was identified as belonging to V. chlorellavorus, while contigs with <180× coverage were assigned to C. vulgaris (Fig. S1). BLASTN (Altschul et al., 1990) (v2.2.29+) using default settings was used to verify that contigs with >180× coverage had homology to bacterial sequences with NCBI's non-redundant database. Additionally, the 16S rRNA gene was identified using Prokka v1.8 ( Seemann, 2014) and a BLASTN search was used to identify the closest neighbour ...
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... rRNA sequences revealed 333 reads mapping to V. chlorellavorus (16 chloroplast, 3 mitochondria). No matches to other microorganisms were identified. Sequence reads were assembled into 113 contigs comprising 3.2 Mbp. Ordination of the data by GC content and mapping read depth revealed a high coverage cluster of contigs comprising ∼94% of the data (Fig. S1). These contigs were inferred to belong to V. chlorellavorus by the presence of a 16S rRNA gene on one of the contigs (see below) and low coverage contigs were inferred to belong to the C. vulgaris by best matches to reference Chlorella genomes. Inspection of the assemblies showed no evidence for microheterogeneity (SNPs, indels) in ...
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... 16S rRNA gene obtained from the draft genome is identical to the reference sequence for V. chlorellavorus ATCC 29753 (acc. HM038000) and comparative analysis confirmed its placement as a deep-branching member of the Cyanobacteria phylum within the class Melainabacteria and order Vampirovibrionales (Soo et al., 2014; Fig. 1B). Importantly, a concatenated gene tree of 109 conserved single copy genes produced a robust topology consistent with the 16S rRNA tree, also placing V. chlorellavorus in the class Melainabacte- ria ( Fig. 1A: Fig. S2). These phylogenetic inferences clearly indicate that V. chlorellavorus is not a member of the Deltaproteobacteria as ...
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... as a deep-branching member of the Cyanobacteria phylum within the class Melainabacteria and order Vampirovibrionales (Soo et al., 2014; Fig. 1B). Importantly, a concatenated gene tree of 109 conserved single copy genes produced a robust topology consistent with the 16S rRNA tree, also placing V. chlorellavorus in the class Melainabacte- ria ( Fig. 1A: Fig. S2). These phylogenetic inferences clearly indicate that V. chlorellavorus is not a member of the Deltaproteobacteria as first suggested (Gromov & Mamkaeva, 1972). (Langille & Brinkman, 2009) with the SIGI-HMM programme (Waack et al., 2006). c Estimated using CheckM v0.9.5 (Parks et al., ...
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... et al., 2014), V. chlorellavorus is missing all recognised photosynthesis genes in- cluding those for Photosystems I and II, chlorophyll and antennae proteins. This supports the hypothesis that photosynthetic cyanobacteria acquired photosystems after diverging from the ancestor of the Melainabacteria (Di Rienzi et al., 2013;Soo et al., 2014; Fig. 1). The V. chlorellavorus genome falls within the size range of previously reported Melainabacteria (1.8 to 5.5 Mbp) but has the highest GC content thus far (51.4%) compared with the GC content of other Melainabacteria who have a range of 27.5% to 49.4%. V. chlorellavorus is the second representative of the class inferred to be capable ...
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... chlorellavorus encodes a flagellum which is also found in some representatives of the order Gastranaerophilales (ACD20, MEL B1 and MEL B2). We inferred a phylogenetic tree for the conserved flagella marker gene, fliI (Minamino & Namba, 2008) and found that the Melainabacteria fliI genes form a monophyletic cluster consistent with their internal branching order in the genome tree ( Fig. 1 and Fig. S6) This association suggests that flagella were present in the cyanobacterial ancestor of the Gastranaerophilales and Vampirovibrionales and were subsequently lost at least once in the Gastranaerophilales (Fig. 1). A global comparison of COG (clusters of orthologous groups) categories revealed that V. chlorellavorus has a functional distribution typical of other Melainabacteria genomes with the exception of genes involved in intracellular trafficking, secretion, and vesicular transport (Fig. S7). ...
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... the Melainabacteria fliI genes form a monophyletic cluster consistent with their internal branching order in the genome tree ( Fig. 1 and Fig. S6) This association suggests that flagella were present in the cyanobacterial ancestor of the Gastranaerophilales and Vampirovibrionales and were subsequently lost at least once in the Gastranaerophilales (Fig. 1). A global comparison of COG (clusters of orthologous groups) categories revealed that V. chlorellavorus has a functional distribution typical of other Melainabacteria genomes with the exception of genes involved in intracellular trafficking, secretion, and vesicular transport (Fig. S7). V. chlorellavorus is overrepresented in this ...
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Some cyanobacteria use light outside the visible spectrum for oxygenic photosynthesis. The far-red light (FRL) region is made accessible through a complex acclimation process that involves the formation of new phycobilisomes and photosystems containing chlorophyll f. Diverse cyanobacteria ranging from unicellular to branched-filamentous forms show...
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... Bacteria can affect phytoplankton in several ways: they either enter phytoplankton cells (Caiola and Pellegrini 1984) such as the nonphotosynthetic cyanobacterium Vampirovibrio chlorellavorus, an obligate parasite of the green alga Chlorella spp. (Soo et al. 2015), engage in cell-to-cell contact (Gumbo and Cloete 2011), or secrete extracellular substances (Choi et al. 2005, Mu et al. 2007) including amino acids, peptides, proteins, or antibiotics that may help lyse the cyanobacterial cells (Gumbo and Cloete 2011). ...
... Scientists have investigated soil cyanobacteria for centuries in these habitats, but seldomly in closed canopy tropical forests. Nowadays, studies imply that soil cyanobacteria, with diverse metabolic capabilities, might occupy much ecological niches in sunless and N-rich environments [22][23][24]. A few studies suggest that there is a higher soil cyanobacterial diversity in tropical forests than expected [5,25,26]. ...
Soil cyanobacteria in tropical forests is understudied despite its important role in soil biochemical process and plant growth. Under a nitrogen (N) deposition background in tropical forests, it is important to learn how soil cyanobacterial communities respond to N deposition and whether phosphorus (P) mediated this response. A fully two-factor (N and P additions) factorial design with four blocks (replicates), each including a 12 × 12 m plot per treatment (Control, +N, +P, and +NP) were established in a tropical secondary forest in 2009. In July of 2022, soil cyanobacteria at 0–10 cm and 10–20 cm depths in the experimental site were collected and analyzed using a metagenomic method. The impact of N and P additions on soil cyanobacteria remained consistent across the different soil depths, even though there was a significant contrast between the two layers. The effect of N addition on soil cyanobacteria did not significantly interact with P addition. N addition increased soil N availability and decreased soil pH but did not significantly affect the soil cyanobacterial community. In contrast, P addition increased soil P availability and soil pH, but decreased soil N availability and substantially changed the soil cyanobacterial community. P addition significantly decreased the abundance of soil cyanobacteria, especially abundant ones. P addition also increased cyanobacterial species richness and Shannon’s diversity, which might be explained by the decline in dominant species and the emergence of new species as nestedness and indicator species analyses suggest. We concluded that (1) soil cyanobacteria in tropical forests exhibits a greater sensitivity to elevated P availability compared to N; (2) an increase in soil P supply may mitigate the advantage held by dominant species, thus facilitating the growth of other species and leading to alterations in the soil cyanobacterial community. This study improves our understanding on how soil cyanobacterial communities in tropical forest responds to N and P addition.
... Affiliation of the predatory Vampirovibrio chlorellavorus with the class Melanibacteria agrees with the nonphotosynthetic nature of this taxon. The genome of Vampirovibrio chlorellavorus was reconstructed in 2009 from the old co-culture with Chlorella vulgaris deposited in 1978 and dealt with in an academic article in 2015 [65]. There have been established strategies to defend commercially produced Chlorella from predation by Vampirovibrio chlorellavorus [66]. ...
Predatory bacteria, along with the biology of their predatory behavior, have attracted interest in terms of their ecological significance and industrial applications, a trend that has been even more pronounced since the comprehensive review in 2016. This mini-review does not cover research trends, such as the role of outer membrane vesicles in myxobacterial predation, but provides an overview of the classification and newly described taxa of predatory bacteria since 2016, particularly with regard to phylogenetic aspects. Among them, it is noteworthy that in 2020 there was a major phylogenetic reorganization that the taxa hosting Bdellovibrio and Myxococcus, formerly classified as Deltaproteobacteria, were proposed as the new phyla Bdellovibrionota and Myxococcota, respectively. Predatory bacteria have been reported from other phyla, especially from the candidate divisions. Predatory bacteria that prey on cyanobacteria and predatory cyanobacteria that prey on Chlorella have also been found. These are also covered in this mini-review, and trans-phylum phylogenetic trees are presented.
... Vampirovibrio chlorellavorus, a nonphotosynthetic Cyanobacteria, is an example of this class of predatory bacteria. Its prey is the microalga Chlorella vulgaris, to which it remains attached and feeds until binary division occurs [18]. ...
Food losses, defined as a reduction in the quantity and quality of food during production and storage, impact food safety and security. Losses caused by plant pathogens are among the most significant. Chemical pesticides have been extensively used to prevent microbial diseases. Their toxicity and reduced efficacy, however, have encouraged investigators to develop alternatives. Alternatives based on microbial biopesticides tend to be safer and more environmentally benign than conventional pesticides. In recent years, formulations based on biopesticides have progressively increased in number and diversity and have attracted commercial interest. Understanding the mechanisms by which biopesticides control the disease is fundamental to achieving optimal disease control. Biocontrol mechanisms can be divided into two main categories: those related to the ability to inhibit pathogens or their virulence factors, and those that enhance host plant fitness and induce disease resistance. Here, the first type of strategy is reviewed, which is directly mediated by physical contact between biocontrol agents and pathogens or indirectly by exposure of a pathogen to antimicrobial or microbial-inhibiting compounds produced by the microbial antagonist. Mechanisms involving physical contact include mycophagy, destruction of pathogenic bacteria by bacteriophages or predation, and disease inhibition by topical applications of specific dsRNA. Indirect mechanisms that do not involve direct contact with a pathogen include the production of antimicrobial compounds, competition, and virulence factor suppression by quorum quenching. These topics are reviewed and discussed.
... While Vampirovibrionia, Sericytochromatia, and Margulisbacteria remain poorly characterized, no genomic evidence has yet emerged for a photosynthetic representative within these clades. The best-described representatives all appear to be part of diverse symbiotic associations within eukaryotes (45, 62,133,141). Cyanobacteria, their close nonphotosynthetic relatives, and Margulisbacteria are part of the Terrabacteria (7) (Figure 4a), a multiphylum-level grouping, which includes Chloroflexota, Firmicutes, and others. ...
Photosystem II is the water-oxidizing and O 2 -evolving enzyme of photosynthesis. How and when this remarkable enzyme arose are fundamental questions in the history of life that have remained difficult to answer. Here, recent advances in our understanding of the origin and evolution of photosystem II are reviewed and discussed in detail. The evolution of photosystem II indicates that water oxidation originated early in the history of life, long before the diversification of cyanobacteria and other major groups of prokaryotes, challenging and transforming current paradigms on the evolution of photosynthesis. We show that photosystem II has remained virtually unchanged for billions of years, and yet the nonstop duplication process of the D1 subunit of photosystem II, which controls photochemistry and catalysis, has enabled the enzyme to become adaptable to variable environmental conditions and even to innovate enzymatic functions beyond water oxidation. We suggest that this evolvability can be harnessed to develop novel light-powered enzymes with the capacity to carry out complex multistep oxidative transformations for sustainable biocatalysis.
Expected final online publication date for the Annual Review of Plant Biology, Volume 74 is May 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
... While Vampirovibrionia, Sericytochromatia, and Margulisbacteria remain poorly characterized, no genomic evidence has yet emerged for a photosynthetic representative within these clades. The best-described representatives all appear to be part of diverse symbiotic associations within eukaryotes (45, 62,133,141). Cyanobacteria, their close nonphotosynthetic relatives, and Margulisbacteria are part of the Terrabacteria (7) (Figure 4a), a multiphylum-level grouping, which includes Chloroflexota, Firmicutes, and others. ...
... Vampirovibrio also contributed to the clustering of T4 fecal communities from those of other time points, however, its role in the mammalian gut microbiome is less clear, as is its classification. The genus Vampirovibrio contains the species Vampirovibrio chlorellavorus which engages in a predatory lifestyle [37] and is still assigned by some classification tools (e.g., the RDP Classifier version 2.13) to the order Bdellovibrionales and family Bdellovibrionaceae, which contain other predatory species of bacteria that have been suggested to have potential as tools in controlling drug-resistant Gram-negative pathogens [38,39]. ...
... However, in 2015 researchers argued that Vampirovibrio belongs to its own family and order within the Melainabacteria taxon [37], which was initially suggested as a sister phylum of Cyanobacteria [40] but has more recently been treated as a class of Cyanobacteria [37]. Members of the Melainabacteria taxon are believed to be non-photosynthetic obligate anaerobic fermenters capable of utilizing a wide variety of carbon sources including polysaccharides, oligosaccharides, simple sugars, amino acids, fatty acids, and organic acids to produce lactate, formate, ethanol, and possibly butyrate [40]. ...
... However, in 2015 researchers argued that Vampirovibrio belongs to its own family and order within the Melainabacteria taxon [37], which was initially suggested as a sister phylum of Cyanobacteria [40] but has more recently been treated as a class of Cyanobacteria [37]. Members of the Melainabacteria taxon are believed to be non-photosynthetic obligate anaerobic fermenters capable of utilizing a wide variety of carbon sources including polysaccharides, oligosaccharides, simple sugars, amino acids, fatty acids, and organic acids to produce lactate, formate, ethanol, and possibly butyrate [40]. ...
Social isolation is detrimental to the health of social mammals inducing neurochemical and hormonal changes related to depression and anxiety, as well as impairments of cardiovascular and immune functioning. Likewise, perceptions of loneliness are increasingly recognized as detrimental to human psychological well-being, cognitive functioning, and physical health. Few studies, however, have examined the impact of social isolation on the intestinal microbiome and metabolome. To better understand the impact of social isolation on these systems, intestinal microbiota, and the systemic impact via the gut–brain axis, we employed prairie voles. Physiological stress on female prairie voles (n = 22) either with a same-sex sibling (n = 11) or in isolation (n =11) for four weeks demonstrated behavioral indicators of increased anxiety and depression in isolated voles (p ≤ 0.01). Bacterial DNA from fecal and colon samples, collected at five time points (T0–4), were sequenced for all nine hypervariable regions of the 16S rRNA gene. Microbiome analyses revealed several differences in gut communities of paired and isolated voles with greater differences at T4. Notably, several taxa associated with host health including Anaerostipes and Lactobacillaceae were more prevalent in paired voles, whereas several taxa associated with known pathogens (e.g., Staphylococcaceae and Enterococcus) or disease were elevated in isolated animals. Similarly, metabolome analyses suggested isolated voles, when compared to paired animals, exhibited differences in metabolites associated with diabetes and colitis. These findings further contribute to our understanding of the harmful effects of social isolation, which cause perturbations in the gut microbiome and serum metabolites.
... Aside from photosynthetic cyanobacteria, the temporal dynamics of recently described clades of non-photosynthetic cyanobacteria (Soo et al., 2015) have been investigated using sedDNA from temperate lake cores (Ibrahim et al., 2021;Salmaso et al., 2018). It was recently suggested that these ancestral cyanobacteria respond to different factors than the photosynthetic lineages (Monchamp et al., 2019), probably due to the fact that they have alternative metabolic pathways. ...
Analyses of sedimentary DNA ( sed DNA) have increased exponentially over the last decade and hold great potential to study the effects of anthropogenic stressors on lake biota over time.
Herein, we synthesise the literature that has applied a sed DNA approach to track historical changes in lake biodiversity in response to anthropogenic impacts, with an emphasis on the past c. 200 years.
We identified the following research themes that are of particular relevance: (1) eutrophication and climate change as key drivers of limnetic communities; (2) increasing homogenisation of limnetic communities across large spatial scales; and (3) the dynamics and effects of invasive species as traced in lake sediment archives.
Altogether, this review highlights the potential of sed DNA to draw a more comprehensive picture of the response of lake biota to anthropogenic stressors, opening up new avenues in the field of paleoecology by unrevealing a hidden historical biodiversity, building new paleo‐indicators, and reflecting either taxonomic or functional attributes.
Broadly, sed DNA analyses provide new perspectives that can inform ecosystem management, conservation, and restoration by offering an approach to measure ecological integrity and vulnerability, as well as ecosystem functioning.
... Rienzi et al. [37] reported that Melainabacteria, a new candidate of Cyanobacteria, has been reported to be able to fix nitrogen and live in the human intestine and other aquatic environments. Soo et al. [38] reported that the Melainabacteria genome does not have the ability to photosynthesis but produces energy through the anaerobic fermentation process. Cyanobacteria in the aquatic environments have been proven to delay the growth of white leg shrimp, suppress haemocyte concentration, and increase phagocytosis of haemocytes, affecting the shrimp immune system [39]. ...
Along with the high demand for shrimp, the production challenges faced by practitioners are increasing in Indonesia, one of which is in Lampung region. Various basic monitoring techniques regarding the environment and farmed shrimp are needed to control production sustainability. This present study aimed to identify the bacterial community profile in the rearing pond water and intestinal tract of Pacific white shrimp Litopenaeus vannamei. Illumina-based sequencing was chosen to determine the bacterial community using the V3-V4 region of the bacterial 16S rRNA gene. Sequence data revealed the differences in bacterial community structure between the rearing water and shrimp intestines. Proteobacteria was the most prevalent phylum in the rearing water (W.B), accounting for 45.29 %, followed by Cyanobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria. In the shrimp intestinal tract (S.B), Cyanobacteria (35.15 %) dominated the microbiota, followed by Proteobacteria, Saccharibacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, TM6 (Dependentiae), and Firmicutes. Cyanobacteria were higher in the shrimp intestines (35.15 %) than in the rearing water (26.63 %). In addition, Escherichia-Shigella was the most common genera in the rearing water and shrimp intestines with different relative abundance. Cyanobacteria and Escherichia-Shigella highly detected in the rearing water and shrimp’s intestines might indicate that pond water had been polluted. Further investigation is necessary on the correlation of Cyanobacteria in the shrimp intestines with water pollution, proven by the dominance of Cyanobacteria and Escherichia-Shigella. These findings provide basic information to enhance our understanding of the microbial community and their roles in the shrimp culture environment to improve the quantity and quality of the yield and support its sustainability. HIGHLIGHTS Bacterial community profile in the rearing water and the intestinal tract of Pacific whiteleg shrimp play important roles in shrimp production Bacterial community structure differed between the rearing water and shrimp intestines Proteobacteria was the most abundant phylum in the rearing water (W.B), while Cyanobacteria dominated the microbiota in the intestinal tract of Pacific whiteleg shrimp Cyanobacteria and Escherichia-Shigella highly detected in the rearing water and shrimp’s intestines might indicate that pond water had been polluted GRAPHICAL ABSTRACT
... Sequences of Vampirivibrionia (in the phylum Cyanobacteria) were also enriched in the bog samples (0.73% in F and 0.24% in others). The only cultured species of this taxon, Vampirovibrio chlorellavorus, is a predator of single-celled green algae Chlorella [62]. This suggests that a predatory lifestyle may be favored in aquatic habitats compared to terrestrial ones. ...
Subtropical montane peatland is among several rare ecosystems that continue to receive insufficient scientific exploration. We analyzed the vegetation types and soil bacterial composition, as well as surface carbon dioxide and methane fluxes along a successional peatland-to-upland-forest series in one such ecosystem in Taiwan. The Yuanyang Lake (YYL) study site is characterized by low temperature, high precipitation, prevailing fog, and acidic soil, which are typical conditions for the surrounding dominant Chamaecyparis obtusa var. formosana forest. Bacterial communities were dominated by Acidobacteriota and Proteobacteria. Along the bog-to-forest gradient, Proteobacteria decreased and Acidobacteriota increased while CO2 fluxes increased and CH4 fluxes decreased. Principal coordinate analysis allowed separating samples into four clusters, which correspond to samples from the bog, marsh, forest, and forest outside of the watershed. The majority of bacterial genera were found in all plots, suggesting that these communities can easily switch to other types. Variation among samples from the same vegetation type suggests influence of habitat heterogeneity on bacterial community composition. Variations of soil water content and season caused the variations of carbon fluxes. While CO2 flux decreased exponentially with increasing soil water content, the CH4 fluxes exhibited an exponential increase together with soil water content. Because YYL is in a process of gradual terrestrialization, especially under the warming climate, we expect changes in microbial composition and the greenhouse gas budget at the landscape scale within the next decades.
