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![Phylogenetic tree highlighting the position of H. ochraceum SMP-2T relative to the other type strains within the genus and the type strains of the other genera within the order Myxococcales. The tree was inferred from 1,463 aligned characters [12,13] of the 16S rRNA gene sequence under the maximum likelihood criterion [14] and rooted in accordance with the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [15] are shown in blue, published genomes in bold.](profile/Jonathan-Eisen-2/publication/49820727/figure/fig1/AS:202579461054474@1425310115983/Phylogenetic-tree-highlighting-the-position-of-H-ochraceum-SMP-2T-relative-to-the-other.png)
Phylogenetic tree highlighting the position of H. ochraceum SMP-2T relative to the other type strains within the genus and the type strains of the other genera within the order Myxococcales. The tree was inferred from 1,463 aligned characters [12,13] of the 16S rRNA gene sequence under the maximum likelihood criterion [14] and rooted in accordance with the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [15] are shown in blue, published genomes in bold.
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Haliangium ochraceum Fudou et al. 2002 is the type species of the genus Haliangium in the myxococcal family 'Haliangiaceae'. Members of the genus Haliangium are the first halophilic myxobacterial taxa described. The cells of the species follow a multicellular lifestyle in highly organized biofilms, called swarms, they decompose bacterial and yeast...
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... is no surprise that these pheno- mena are regulated by sophisticated networks including two-component regulatory systems [11]. Figure 1 shows the phylogenetic neighborhood of H. ochraceum SMP-2 T in a 16S rRNA based tree. The sequences of the two 16S rRNA gene copies in the genome of do not differ from each other, and do not differ from the previously published 16S rRNA sequence of DSM 14365 (AB016470). ...Similar publications
Covering: 2011-July 2016Myxobacteria are a rich source for structurally diverse secondary metabolites with intriguing biological activities. Here we report on new natural products that were isolated from myxobacteria in the period of 2011 to July 2016. Some examples of recent advances on modes-of-action are also summarised along with a more detaile...
The diversity and distribution of bacteria are crucial for our understanding of their ecological importance and application potential. Myxobacteria are fascinating prokaryotes with multicellular behaviors and a potent capacity for producing secondary metabolites, and have a wide range of potential applications.
Myxobacteria are abundant micropredators in soil, and are social bacteria with multicellular behavior and producers of versatile secondary metabolites. The interaction between predator and prey populations is an important component in the soil microbial food web, and this is expected to shape the composition and dynamics of microbial communities. H...
Bacteria glide across solid surfaces by mechanisms that have remained largely mysterious despite decades of research. In the deltaproteobacterium Myxococcus xanthus, this locomotion allows the formation stress-resistant fruiting bodies where sporulation takes place. However, despite the large number of genes identified as important for gliding, no...
Some bacterial clades are important sources of novel bioactive natural products. Estimating the magnitude of chemical diversity available from such a resource is complicated by issues including cultivability, isolation bias and limited analytical data sets. Here we perform a systematic metabolite survey of ~2300 bacterial strains of the order Myxoc...
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... This group of bacteria displays genes encoding key enzymes that took part in the production of polyketide and peptide metabolites, including polyketide synthases and nonribosomal peptide synthases. They also have the ability to decompose macromolecules such as starch, DNA, casein, gelatine, and chitin [37]. ...
In wastewater treatment plants, the stability of the related microbiota is pivotal for a steady and appropriate operation in biological wastewater treatment (BWT). The interactions between phages, which are high in amounts and diversity, and their particular hosts are significant due to their specificity in this microbial community. As drivers of diversity, phages are capable of changing the microbial structure by affecting host cells. This study aimed to enhance the stability of the functional microbiota, a primary concern of BWT, by evaluating the influence of bioaugmentation with bacteriophage cocktails. The sequencing data revealed significant alterations in the entire microbiome, including microeukaryotes, induced by the bacteriophages. These alterations led to a reduction in opportunistic microorganisms while preserving the beneficial ones. The genus Proteobacteria was found unaffected by three antibiotics in the bioreactor due to its antibiotic-resistant members, leading to its further growth, while the antibiotic-sensitive genus decreased in quantity. Furthermore, the phages notably influenced the metabolic pathway such as nitrogen, carbohydrate, and amino acid metabolisms by eliminating opportunistic microbes and providing improved growth conditions to bacterial species that are essential for effective reactor performance and wastewater treatment.
... Pedomicrobium species were identified as the primary contributors to affect the quality of wasted water polluted by manganese (Larsen et al., 1999). Haliangium is a genus of bacteria from the Kofleriaceae family that produces antifungal chemicals that may enhance the immunological response of spiders under adverse conditions (Ivanova et al., 2010). Therefore, the different expression patterns of these identified genera may be involved in the metabolism of cuticles, immune responses, and survival of spiders under Cd stress. ...
Although research into how spiders respond to cadmium (Cd)-induced toxicity is ongoing, little is known about the effects of Cd contamination on the exogenous microorganisms of spiders. The current study used 16 S rRNA gene sequencing to evaluate the richness and structure of external bacterial communities in the wolf spider Pardosa pseudoannulata under long-and short-term Cd stress. Our results showed that Proteobacteria and Acidibacter were the dominating bacterial phylum and genus. The alpha diversity analysis showed that the high background of Cd concentration (Cd) reduced bacterial alpha diversity, and short-term Cd (SCd) stress elevated bacterial richness and diversity. Hub bacterial genera, including Stenotrophobacter, Hymenobacter, Chitinophaga, and Bryobacter, were identified by co-occurrence network analysis and showed high connectance with other bacterial genera. Further investigation revealed 15 and 14 bacterial taxa that were classified distinctively under SCd and Cd stresses. Interestingly, functional prediction analysis showed that Cd stress enhanced some crucial pathways involved in specialized functions, including manganese oxidation and aromatic compound degradation. Random forest and correlation analyses found that the spider's molting time was the dominant driver affecting bacterial phyla (i.e., Proteobacteria and Planctomycetes) and genera (e.g., Acidibacter, Reyranella, and Haliangium). Collectively, this comprehensive analysis creates new perspectives to investigate the divergent responses of microbial communities in the spiders' external habitat under Cd stress, and provides valuable viewpoints for Cd pollution evaluation and control.
... This study explored 61 myxobacterial genomes, distributed within three suborders and nine families (58)(59)(60)(61)(62)(63)(64)(65)(66)(67)(68)(69)(70)(71), in addition to 59 outgroup genomes [members from 32 non-Myxococcales Deltaproteobacteria, 4 α-, 6 β-, 9 γ-, 4 £-proteobacteria, 2 Firmicutes, 1 Actinobacteria, and 1 FCB (Fibrobacteres, Chlorobi, and Bacteroidetes) group organism]. Highly conserved gapless concatenated alignment of 26 housekeeping protein sequences (68,72) was subjected to RAxML to build a maximum likelihood phylogenetic tree using JTT Substitution Matrix and 100 bootstrap values (73). ...
The predatory deltaproteobacterium Myxococcus xanthus uses a helically-trafficked motor at bacterial focal-adhesion (bFA) sites to power gliding motility. Using total internal reflection fluorescence and force microscopies, we identify the von Willebrand A domain-containing outer-membrane (OM) lipoprotein CglB as an essential substratum-coupling adhesin of the gliding transducer (Glt) machinery at bFAs. Biochemical and genetic analyses reveal that CglB localizes to the cell surface independently of the Glt apparatus; once there, it is recruited by the OM module of the gliding machinery, a heteroligomeric complex containing the integral OM β barrels GltA, GltB, and GltH, as well as the OM protein GltC and OM lipoprotein GltK. This Glt OM platform mediates the cell-surface accessibility and retention of CglB by the Glt apparatus. Together, these data suggest that the gliding complex promotes regulated surface exposure of CglB at bFAs, thus explaining the manner by which contractile forces exerted by inner-membrane motors are transduced across the cell envelope to the substratum.
... PGPR are considered relevant for agriculture, allowing a more limited use of fertilizers, since they can be used as biofertilizers and bio-stimulants (Martins da Costa 2018;Htwe et al. 2019). Haliangium appears as the most dominant genera from the Myxococcales, which is characterized by their multicellular life form, organized in biofilms, and by their production of antifungal molecules (Ivanova et al. 2010). The lower abundance of Rhizobiales (particularly from the Beijerinckiaceae family) in the SC condition can be due to the negative correlation of this family with the pH of the soil, which was higher at this level of tree coverage (Dedysh et al. 2016). ...
Abstract Soil biota is considered a crucial component of soil health. Currently, the soil microbiota and its genomic material (microbiome) have received increasing attention due to their role on sustainable nutrient availability. However, in agroforestry systems,
little information is available on the effect of tree cover on natural microbial assemblies and its potential impact on soil health and production. From this perspective, we present the initial and novel results of the metagenomic-based characterization of microbial
diversity in the soil of a Nothofagus-based silvopastoral system with three different shade conditions (open, semi open, and semi closed), that were obtained simultaneously by the massive sequencing of ribosomal genes for Bacteria, Archaea, Eukarya, and of the ribosomal Internal Transcribed Spacer (ITS3-4) for Fungi. In the temperate SPS, the dominant bacteria phylum was Proteobacteria particularly from the order Rhizobiales, while the fungal community was dominated by Ascomycota and Basidiomycota. A low
presence of archaea and eukaryotes was also observed. The semi open shade condition exhibited the highest diversity of microorganisms of all the treatments. This condition also promoted a greater specific production of grass. Our preliminary results not only represent the first multi-domain microbial inventory in the study area, but they also highlight the need to consider the microbial assemblies in the design and management of
soil-based production systems, and the conservation of biodiversity in ecosystems.
Keywords Silvopasture � Roble � Nothofagus � Soil microbiome � Microbial diversity
... For P. pacifica SIR-1, the L50 value is 40 and N50 value is 82,268 bp which are typical values for large myxobacterial genomes. The complete genome of another marine myxobacterium, Haliangium ochraceum SMP-2, was published shortly after that of P. pacifica SIR-1 [23]. Although myxobacteria have traditionally been viewed as soil bacteria, an increasing number of marine examples have been described. ...
... SMP-2 was isolated from seaweed and grows optimally at 2% (w/v) NaCl. As is typical for myxobacteria, it is predatory and forms multicellular fruiting bodies, with a large (9.5 Mbp), high %GC (69.5%) genome [23]. ...
Myxobacteria are fascinating and complex microbes. They prey upon other members of the soil microbiome by secreting antimicrobial proteins and metabolites, and will undergo multicellular development if starved. The genome sequence of the model myxobacterium Myxococcus xanthus DK1622 was published in 2006 and 15 years later, 163 myxobacterial genome sequences have now been made public. This explosion in genomic data has enabled comparative genomics analyses to be performed across the taxon, providing important insights into myxobacterial gene conservation and evolution. The availability of myxobacterial genome sequences has allowed system-wide functional genomic investigations into entire classes of genes. It has also enabled post-genomic technologies to be applied to myxobacteria, including transcriptome analyses (microarrays and RNA-seq), proteome studies (gel-based and gel-free), investigations into protein–DNA interactions (ChIP-seq) and metabolism. Here, we review myxobacterial genome sequencing, and summarise the insights into myxobacterial biology that have emerged as a result. We also outline the application of functional genomics and post-genomic approaches in myxobacterial research, highlighting important findings to emerge from seminal studies. The review also provides a comprehensive guide to the genomic datasets available in mid-2021 for myxobacteria (including 24 genomes that we have sequenced and which are described here for the first time).
... Adaptation without spacer loss would presumably lead to ever-longer arrays, but among genomes sequenced so far, extremely long arrays are relatively rare. Arrays with greater than 100 spacers are observed; Haliangium ochraceum is a notable example, with a single array of 587 spacers and two other arrays measuring 189 and 36 spacers, respectively (Ivanova et al., 2010;Pourcel et al., 2020). However, a typical array contains fewer than 50 spacers in bacteria and fewer than 100 in archaea (Horvath et al., 2008;Mangericao et al., 2016;Pourcel et al., 2020). ...
CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated genes) is a type of prokaryotic immune system that is unique in its ability to provide sequence-specific adaptive protection, which can be updated in response to new threats. CRISPR-Cas does this by storing fragments of DNA from invading genetic elements in an array interspersed with short repeats. The CRISPR array can be continuously updated through integration of new DNA fragments (termed spacers) at one end, but over time existing spacers become obsolete. To optimize immunity, spacer uptake, residency, and loss must be regulated. This mini-review summarizes what is known about how spacers are organized, maintained, and lost from CRISPR arrays.
... The genus Thiobacillius, which is associated with the redox of sulphur species, makes sulphate nutrients available for plant uptake (Pronk et al., 1990). In addition, Methylobacterium facilitates plant survival in a range of harsh environments such as desiccation or high salinity by producing biofilms (Chen et al., 2003;Ivanova et al., 2010;Yano et al., 2012), while Pseudomonas and Flavobacterium participate in plant disease suppression (Hu et al. 2017;Kwak et al., 2018;Weller, 2007), and the genera Rhodoferax, a phototrophic bacteria, is related to plant photosynthesis so as to stimulate plant growth (Hiraishi et al., 1991). ...
The northeast region of China is an important grain growing area. However, severe soil salinization in the region impairs plant production. In the present study, organic fertilizer application (composted poultry manure) was evaluated as a potential strategy for remediating saline‐alkali soil and promoting rice growth. Following continuous organic fertilizer application for 4 years, the contents of basic cations, including sodium (Na⁺) and chlorine cations (Cl‐), decreased significantly (P < 0.05) (soil Na+ decreased from 24.3 mg/kg to 21.8 mg/kg and soil Cl‐ decreased from 570.4 mg/kg to 38.5 mg/kg), while soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), available nitrogen (AN), and available potassium (AK) were markedly increased (especially for soil AK, which increased from 85.8 mg/kg to 141.7 mg/kg) compared to the treatment without organic fertilizer application. In addition, the relative abundance of plant growth‐promoting bacteria such as Thiobacillius, Methylobacter, Rhodoferax, Lysobacter, and Flavobacterium increased significantly, whereas halophilic genera (Nitriliruptor, Mongoliicoccus, Litoribacter, Halomonas, and Aliidiomarina) decreased markedly. Bacterial diversity also increased significantly, with data analysis suggesting that such shifts translated into more abundant plant‐growth‐related gene functions. According to structural equation modelling results, soil bacterial diversity was a key factor driving the maintenance of healthy plant growth in saline‐alkali soil. These results suggested that organic fertilizers could improve the physicochemical properties of saline‐alkali soil by altering interactions between rice plants and bacteria, for example, via the recruitment of specific beneficial microbial communities to increase their salinity‐alkali stress tolerance, and, in turn, promote their growth.
... Forty order Myxococcales genomes [83][84][85][86][87][88][89][90][91][92][93][94][95][96][97][98] were downloaded from NCBI followed by RASTbased gene prediction and annotation [99]. ) were identified, and the protein information was extracted. Based on the identified proteins and the location in the genome of their coding sequences, clusters were manually curated. ...
The development of multicellularity is a key evolutionary transition allowing for differentiation of physiological functions across a cell population that confers survival benefits; among unicellular bacteria, this can lead to complex developmental behaviors and the formation of higher-order community structures. Herein, we demonstrate that in the social δ-proteobacterium Myxococcus xanthus, the secretion of a novel biosurfactant polysaccharide (BPS) is spatially modulated within communities, mediating swarm migration as well as the formation of multicellular swarm biofilms and fruiting bodies. BPS is a type IV pilus (T4P)-inhibited acidic polymer built of randomly acetylated β-linked tetrasaccharide repeats. Both BPS and exopolysaccharide (EPS) are produced by dedicated Wzx/Wzy-dependent polysaccharide-assembly pathways distinct from that responsible for spore-coat assembly. While EPS is preferentially produced at the lower-density swarm periphery, BPS production is favored in the higher-density swarm interior; this is consistent with the former being known to stimulate T4P retraction needed for community expansion and a function for the latter in promoting initial cell dispersal. Together, these data reveal the central role of secreted polysaccharides in the intricate behaviors coordinating bacterial multicellularity.
... Considering the comparative transcriptomic studies of M. xanthus [49], and relevant previous literature, a set of 132 proteins has been selected for this study, known to be involved in development specific functions. Most of these proteins have homologs in other myxobacterial genomes too (unpublished data) such as M. fulvus [50], M. hansupus [51], Stigmatella aurantiaca [49], Archangium gephyra [52], Anaeromyxobacter dehalogenans [53], Haliangium ochraceum [54], Sandaracinus amylolyticus [55] and Sorangium cellulosum [56]. Here we performed the comparative transcriptional expression studies in M. xanthus stationary, vegetative and peripheral rod cells to understand the level of expression of these development genes (Tables 5 and 6). ...
In response to nutrient deprivation, the ubiquitous Gram-negative soil bacterium Myxococcus xanthus undergoes a well-characterized developmental response, resulting in the formation of a multicellular fruiting body. The center of the fruiting body consists of myxospores; surrounding this structure are rod-shaped peripheral cells. Unlike spores, the peripheral rods are a metabolically active cell type that inhabits nutrient-deprived environments. The survival characteristics exhibited by peripheral rods, protection from oxidative stress and heat shock, are common survival characteristics exhibited by cells in stationary phase including modifications to morphology and metabolism. Vegetative M. xanthus cells undergo a number of physiological changes during the transition into stationary phase similar to other proteobacteria. In M. xanthus, stationary-phase cells are not considered a component of the developmental response and occur when cells are grown on nutrient-rich plates or in dispersed aqueous media. However, this cell type is not routinely studied and little of its physiology is known. Similarities between these two stress-induced cell types led to the question of whether peripheral rods are actually a distinct developmental cell type or simply cells in stationary phase. In this study, we examine the transcriptome of peripheral rods and its relationship to development. This work demonstrates that peripheral rods are in fact a distinct developmentally differentiated cell type. Although peripheral rods and stationary phase cells display similar characteristics, each transcriptomic pattern is unique and quite different from that of any other M. xanthus cell type.
... The strain NS21 T , in which the latA gene encodes a RoxA ortholog, grows on a NR-overlay agar medium forming a clearing zone on it, and depolymerizes poly(cis-1,4-isoprene) [19,20]. However, knowledge of the whole genome sequences of gram-negative NR-degrading bacteria is limited except for that of Haliangium ochraceum DSM 14365 [21]. To get novel insights into the NR degradation pathway of gram-negative bacteria, the complete genome sequence of R. gummiphilus NS21 T was determined and the genes involved in NR degradation were identified. ...
Gram-negative natural rubber-degrader, Rhizobacter gummiphilus NS21 T , which was isolated from soil in the botanical garden in Japan, is a newly proposed species of genus of Rhizobacter. It has been reported that the latA1 gene is involved in the natural rubber degradation in this strain. To gain novel insights into natural rubber degradation pathway, the complete genome sequence of this strain was determined. The genome of strain NS21 T consists of 6,398,096 bp of circular chromosome (GenBank accession number CP015118.1) with G + C content of 69.72%. The genome contains 5687 protein-coding and 68 RNA genes. Among the predicted genes, 4810 genes were categorized as functional COGs. Homology search revealed that existence of latA1 homologous gene (latA2) in this genome. Quantitative reverse-transcription-PCR and deletion analyses indicated that natural rubber degradation of this strain requires latA2 as well as latA1.
