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(a) Pseudoplasmodia of Byssovorax cruenta By c2 T may eventually contract into bright-red knobs resembling Myxococcus fruiting bodies. Bar, 200 mm. A similar image in colour is available as Supplementary Fig. S2 in IJSEM Online. (b) In contrast to Byssovorax, Polyangium strains as a rule produce compact pseudoplasmodia, and only late in development as an initiation of fruiting body formation. Note short slime tails at the rear ends of the cell masses and depressions in the agar surface. Bar, 380 mm.
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A rare, cellulose-decomposing myxobacterium is described, and a new genus name, Byssovorax, is proposed for it. The organism is almost certainly identical to the species 'Myxococcus cruentus' Thaxter 1897, and that species epithet is therefore revived for the novel bacterium: the type strain of Byssovorax cruenta gen. nov., sp. nov., nom. rev. is s...
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Myxobacteria, a group of Gram-negative aerobes, belong to the class delta-proteobacteria and order Myxococcales. Unlike anaerobic delta-proteobacteria, they exhibit several unusual physiogenomic properties like gliding motility, desiccation-resistant myxospores and large genomes with high coding density. Here we report a 9.5 Mbp complete genome of...
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... Similarly, e[CO 2 ] increased the DNRA rate by 141 % in grassland (Müller et al., 2009). Myxococcaceae uses water-insoluble organic substances such as cellulose as nutrients (Reichenbach et al., 2006), and e [CO 2 ] increased the relative abundance of Myxococcaceae and promoted soil dissimilatory reduction. In addition, most of the microorganisms involved in DNRA are heterotrophic and require organic carbon as an electron donor (Schmidt et al., 2011;Sotta et al., 2008). ...
Climate change scenarios forecast both increase in atmospheric CO 2 concentration ([CO 2 ]) and temperature. Elevated [CO 2 ] (e[CO 2 ]) and soil temperature (eST) significantly increased plant growth and nitrogen (N) uptake. However, studies on the combined effect of these factors on soil N transformation and microbial community are scarce in agricultural intensification. In the present work, we cultivated cucumber plants under e[CO 2 ] or/ and eST, followed by a paired labeling 15 N tracer experiment (15 NH 4 NO 3 and NH 4 15 NO 3) to quantify soil gross N transformation rates. Results showed that e[CO 2 ] decreased soil gross N nitrification rate, indicated by a decline in ammonia-oxidizing bacteria (amoA-AOB) and nitrite oxidoreductase alpha subunit (nxrA) gene copy numbers, and changed microbial taxonomic composition under ambient soil temperature (aST). Furthermore, eST increased chitinase gene (chiA) and amoA-AOB gene copy numbers and alpha diversity and changed the microbial taxonomic composition to improve soil gross N mineralization and nitrification rates. The combination of e[CO 2 ] and eST promoted soil gross N mineralization, nitrification, and immobilization rates compared with ambient [CO 2 ] and aST. The study showed that the combination of e[CO 2 ] and eST increased the primary gross N transformation rates and accelerated soil N circulation, which could ensure plant N demand. Therefore, combining e[CO 2 ] and eST provided a promising way to help cultivators promote vegetable growth in winter, mitigate soil N loss, and achieve sustainable development in greenhouse vegetable cultivation.
... Compared with the grass soils at low N in this study, a high abundance of Pedobacter sp. and a lower abundance of Byssovorax sp. were generally found in legume soils. Pedobacter sp. has been described as an endophytic bacteria preferentially associating with legumes (Dudeja and Giri 2014;Piechulla et al. 2017;Wemheuer et al. 2017), and Byssovorax sp. was shown to be a cellulose decomposer also able to use nitrate as a source of N (Reichenbach et al. 2006). Our results above imply that N fertilisation and biological N fixation have strong effects on bacterial communities, especially on nitrifying and denitrifying genera. ...
Context There is concern that the introduction of ‘novel’ plant germplasm/traits could outpace our capacity to measure and so assess their impacts on soil microbial communities and function. Aim This study aimed to investigate the effects of plant species/functional traits, nitrogen (N) fertilisation and endophyte infection on grassland soil microbial communities within a short time span of 2 years. Methods Two field experiments with monoculture plots were conducted in a common soil. Experiment 1 compared grasses and legumes, using two cultivars of perennial ryegrass (Lolium perenne) that varied in fructan content, along with the legumes white clover (Trifolium repens) and bird’s-foot trefoil (Lotus pedunculatus) that varied in tannin content. Grass treatments received high and low N application levels. Experiment 2 compared the presence/absence of Epichloë strains in ryegrass, tall fescue (Schedonorus phoenix) and meadow fescue (Schedonorus pratensis). Soil microbial communities were analysed by using high-throughput sequencing of DNA isolated from bulk soil cores. Key results Higher abundance of ligninolytic fungi was found in grass soils and pectinolytic fungi in legume soils. Levels of N fertilisation and fructan in ryegrass had only minor effects on soil fungal communities. By contrast, N fertilisation or fixation had a strong effect on bacterial communities, with higher abundance of nitrifiers and denitrifiers in high-N grass soils and in legume soils than in low-N grass soils. Epichloë affected soil microbiota by reducing the abundance of certain fungal phytopathogens, increasing mycorrhizal fungi and reducing N-fixing bacteria. Conclusions Chemical composition of plant cell walls, which differs between grasses and legumes, and presence of Epichloë in grasses were the main drivers of shifts in soil microbial communities. Implications Impacts of farming practices such as mono- or poly-culture, N fertilisation and presence of Epichloë in grasses on soil microbial communities should be considered in pasture management.
... Due to the difficulties in isolation, only seven families and 19 genera have been validly published in the LPSN database. 1 According to their nutritional behaviors and specialization in the degradation of biomacromolecules, members of the phylum Myxococcota are divided into two groups: proteolytic and cellulolytic myxobacteria (Reichenbach et al., 2006;Mohr et al., 2018). ...
... homologue genes of Tad-like pilus were not present in the two genera Sorangium and Polyangium of the order Polyangiales, and the two orders Haliangiales and Nannocystales ( Figure 5), indicating these species may have different predatory strategies (or none whatsoever) (Reichenbach et al., 2006). Moreover, the Tad-like genes were also present in the Bdellovibrionales, Bradymonadales and Herpetosiphonales ( Figure 5). ...
Myxobacteria are part of the phylum Myxococcota, encompassing four orders. Most of them display complex lifestyles and broad predation profiles. However, metabolic potential and predation mechanisms of different myxobacteria remains poorly understood. Herein, we used comparative genomics and transcriptomics to analyze metabolic potentials and differentially expressed gene (DEG) profiles of Myxococcus xanthus monoculture (Mx) compared to coculture with Escherichia coli (MxE) and Micrococcus luteus (MxM) prey. The results showed that myxobacteria had conspicuous metabolic deficiencies, various protein secretion systems (PSSs) and the common type II secretion system (T2SS). RNA-seq data demonstrated that M. xanthus overexpressed the potential predation DEGs, particularly those encoding T2SS, the tight adherence (Tad) pilus, different secondary metabolites (myxochelin A/B, myxoprincomide, myxovirescin A1, geosmin and myxalamide), glycosyl transferases and peptidase during predation. Furthermore, the myxalamide biosynthesis gene clusters, two hypothetical gene clusters and one arginine biosynthesis clusters were highly differential expressed in MxE versus MxM. Additionally, homologue proteins of the Tad (kil) system and five secondary metabolites were in different obligate or facultative predators. Finally, we provided a working model for exhibiting multiple predatory strategies when M. xanthus prey on M. luteus and E. coli. These results might spur application-oriented research on the development of novel antibacterial strategies.
... Technological and methodological advances over decades have introduced challenges to traditionally accepted theories and premises related to predatory myxobacteria. The transition from morphology-based classification of myxobacteria to a combination of traditional methods and comparative genomics has resulted in various taxonomic reassignments and proposed updates (Awal et al., 2017;Waite et al., 2020;Ahearne et al., 2021), and descriptions from newly discovered myxobacteria often include predation data (Figure 2; Fudou et al., 2002;Sanford et al., 2002;Iizuka et al., 2003aIizuka et al., ,b, 2013Reichenbach et al., 2006;Garcia et al., 2009Garcia et al., , 2014Garcia et al., , 2016Mohr et al., 2012Mohr et al., , 2018aYamamoto et al., 2014;Sood et al., 2015;Awal et al., 2016Awal et al., , 2017Moradi et al., 2017;Garcia and Muller, 2018;Chambers et al., 2020;Wang et al., 2021a;Zhou et al., 2021). Myxobacteria are often split into two groups based on presumed nutritional preferences or needs, predatory myxobacteria that acquire nutrients from prey lysate and cellulolytic myxobacteria (Shimkets et al., 2006;Mohr, 2018). ...
Myxobacteria are excellent model organisms for investigation of predator-prey interactions and predatory shaping of microbial communities. This review covers interdisciplinary topics related to myxobacterial predation and provides current concepts and challenges for determining predatory performance. Discussed topics include the role of specialized metabolites during predation, genetic determinants for predatory performance, challenges associated with methodological differences, discrepancies between sequenced and environmental myxobacteria, and factors that influence predation.
... In future studies, this may prove as a crucial clue in identifying its role as a novel species in the degradation of paper pulp. There are lot of known cellulose degraders in D1 (Bacillus foraminis, Byssovorax cruenta, Burkholderia tuberum, Bacteroides fragilis, Bacillus selenatarsenatis, Ammoniphilus oxalaticus etc.) [39][40][41][42][43][44] when compared to D2 (Altererythrobacter epoxidivorans etc.) [45]. Further, D2 can be used as potent sample for identifying novel cellulose degraders as the results above suggest that D2 still remains unexplored. ...
Microbial prospection and evaluation of different novel cellulases requires a comprehensive biomass degrading microbial diversity. For studying microbial ecology of uncultivable microbes, the most potent approach would be high-throughput sequencing. In the present study, with the aim to identify potent cellulose degrading microbial diversity, samples were collected from a 50-year-old saw mill soil at two different depths of 4 cms (D1) and 12 cms (D2) from the ground level. Amplicon metagenomics was performed from the collected samples using Illumina Miseq platform followed by analysis using QIIME and MG-RAST. More than 75% of the microbiota was common to both the studied samples, with hits corresponding to 12 different phyla including unclassified bacteria as the most dominant followed by Proteobacteria. The most abundant genera were falling under four major phyla viz., Proteobacteria, Actinobacteria, Unclassified bacteria and Verrucomicrobia. Results revealed that there are 14 species unique to D1 and 9 unique to D2. D1 has abundant cellulose degraders (Bacillus foraminis, Byssovorax cruenta, Burkholderia tuberum, Bacteroides fragilis, Bacillus selenatarsenatis, Ammoniphilus oxalaticus etc.) when compared to D2 (Altererythrobacter epoxidivorans etc.). In context to the site under study, the results summarized in the work provide a primary snapshot of the microbial composition in sawmill soil and suggests that bio-prospection of the studied microbiome for carbohydrate degrading genes would yield potentially novel genes due to the abundance of unclassified and uncultured bacteria. Further, gene mining and expression study from the studied microbiota would yield potential enzymes for agroindustrial applications.
... At the high resolution, sequences of the heavy DNA fractions extracted from microcosms treated with 13 C-cellulose were related to cellulolytic bacteria of the order Myxococcales (2.3%), the families Ruminococcaceae (15.5%) and Lachnospiraceae (6.5%), and the genus Paenibacillus (6.9%) (Fig. 5c). These bacteria possess gene-encoding plant cell walldegrading enzymes and can metabolize hemicellulose and/or cellulose (Flint et al. 2012;Miron and Ben-Ghedalia 1992;Moon et al. 2011;Ozbayram et al. 2017;Reichenbach et al. 2006). In addition, members having gene-encoding CAZymes are involved in the cleavage of glycosidic bonds present in xylan and cellulose (Coutinho et al. 2009). ...
To determine bacterial communities involved, directly or indirectly, in the anaerobic degradation of cellulose, we conducted a microcosm experiment with soil treated with ¹³C-cellulose, ¹²C-cellulose, or without cellulose with analyses of DNA-based stable isotope probing (DNA-SIP), real-time quantitative PCR, and high-throughput sequencing. Firmicutes, Actinobacteria, Verrucomicrobia, and Fibrobacteres were the dominant bacterial phyla-degrading cellulose. Generally, bacteria possessing gene-encoding enzymes involved in the degradation of cellulose and hemicellulose were stimulated. Phylotypes affiliated to Geobacter were also stimulated by cellulose, probably due to their role in electron transfer. Nitrogen-fixing bacteria were also detected, probably due to the decreased N availability during cellulose degradation. High-throughput sequencing showed the presence of bacteria not incorporating ¹³C and probably involved in the priming effect caused by the addition of cellulose to soil. Collectively, our findings revealed that a more diverse microbial community than expected directly and indirectly participated in anaerobic cellulose degradation.
... In 2006, Reichenbach et al. reclassified 'M. cruentus' as Byssovorax cruenta [5]. The genus Sorangium is remarkable for various reasons: most myxobacteria have large genomes (between 9-12 Mbp), however, Sorangium cellulosum strain Soce 56 has a genome size of 13 Mbp [6] and Minicystis rosea (DSM 24000; accesion no. ...
Seventy-three strains of Sorangium have been isolated from soil samples collected from all over the world. The strains were characterized using a polyphasic approach and phenotypic, genotypic and chemotype analyses clarified their taxonomic relationships. 16S rRNA, xynB1, groEL1, matrix-assisted laser desorption/ioniziation time-of-flight mass spectrometry and API-ZYM analyses were conducted. In addition, from selected representative strains, fatty acids, quinones and phospholipids were analysed. In silico DNA-DNA hybridization and DNA-DNA hybridization against the current type species of Sorangiumcellulosum strain Soce 1871T (DSM 14627T) completed the analyses. Finally, our study revealed seven new species of Sorangium: Sorangium ambruticinum (Soce 176T; DSM 53252T, NCCB 100639T, sequence accession number ERS2488998), Sorangium arenae (Soce 1078T; DSM 105768T, NCCB 100643T, ERS2489002), Sorangium bulgaricum (Soce 321T; DSM 53339T, NCCB 100640T, ERS2488999), Sorangium dawidii (Soce 362T; DSM 105767T, NCCB 100641T, ERS2489000), Sorangium kenyense (Soce 375T; DSM 105741T, NCCB 100642T, ERS2489001), Sorangium orientale (Soce GT47T; DSM 105742T, NCCB 100638T, ERS2501484) and Sorangium reichenbachii (Soce 1828T; DSM 105769T, NCCB 100644T, ERS2489003).
... The microbial communities in S S2 , S S3 and S S4 all were dominated by heterotrophic bacteria with a proportion of 31.58% (Fig. 5A), 37.31% (Fig. 5B) and 33.54% (Fig. 5C), respectively, resulting in the well COD removal in the UMBR throughout the 216-days performance (Fig. 2E). Many strict aerobic populations were found in S S2 , S S3 and S S4 with a total proportion of 3.95% (Fig. 5A), 10.21% (Fig. 5B) and 12.39% (Fig. 5C), respectively, such as Variovorax (Yoon et al., 2006), Bryobacter (Kulichevskaya et al., 2010), Owenweeksia (Shahina et al., 2013), Atopococcus (Collins et al., 2005), Parasegetibacter (Zhang et al., 2009), Fluviicola (Yang et al., 2014a, Pirellula (Glöckner et al., 2003), Povalibacter (Nogi et al., 2014), Turneriella (Stackebrandt et al., 2013), Shinella (Matsui et al., 2009), Chryseolinea (Zhong et al., 2016), Roseomonas (Dé et al., 2004), Polyangium (Reichenbach et al., 2006), Sphaerobacter (Pati et al., 2010), Tahibacter (Wu et al., 2015b), Bdellovibrio (Stolp and Starr, 1963), Dongia (Liu et al., 2010) and Prosthecobacter (Takeda et al., 2008). The commensalism of various aerobic and anaerobic populations in the biofilm laid the foundation for the synchronous biological processes of COD removal, nitrification and denitrification, and anammox. ...
... Here, we report on isolation of soil bacteria from goldsmith contaminated site that are resistant to MWCNTs and identified as Trabusiella guamensis which belongs to Enterobacteriaceae family and resembles Salmonella subgroups. The T. guamensis finds niche in a wide variety of environments including marine sediments, various fish species, ocean water and spoiled foods [19,20]. The isolated bacteria were enriched with MWCNTs to induce their strong NMs resistance property. ...
In this study, soil bacteria were isolated from nanomaterials (NMs) contaminated goldsmith site and enriched in the presence of multi-walled carbon nanotubes (MWCNTs) in order to obtain resistant bacteria. The isolated resistant bacteria were biochemically and genetically identified as Trabusiella guamensis. Redox-enzyme activity and cell viability assay showed molecular adaptation and no membrane damage in resistant bacteria under MWCNTs stress. The resistant bacteria were allowed to interact with engineered MWCNTs in order to study the bio-transformation in their structure. Raman spectra of bio-transformed MWCNTs revealed increased intensity ratio of ID/IG with subsequent formation of CO and COOH groups on the outer walls of nanotubes that were also confirmed by Fourier transform infrared (FTIR) results. X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and ultraviolet-visible spectroscopy (UV-vis) analysis of bio-transformed MWCNTs revealed surface oxidation of CNTs. The structural changes in concentric walls were also evident from transmission electron microscopy (TEM) images. Our results demonstrated that the biotransformation of MWCNTs was mediated by resistant bacteria through oxidation process. The presented study showed an effective methodology that utilizes NMs resistant microbes for bio-transformation of MWCNTs in different biological settings which will have impact on "green nanotechnology".
... This is also true for their taxonomic annotation, as cellulolytic microorganisms have been found in the phyla of Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria (Anderson et al. 2012;Berlemont and Martiny 2013;Nyyssönen et al. 2013;Woo et al. 2013). Also the order of Actinomycetales contains well known cellulose degraders (Solans and Vobis 2003;Větrovský, Steffen and Baldrian 2014), as does the order of Myxococcales (Reichenbach et al. 2006). ...
Incorporation of plant litter is a frequent agricultural practice to increase nutrient availability in soil and heavily relies on the activity of cellulose degrading microorganisms. Here we address the question how different tillage treatments affect soil microbial communities and their cellulose degrading potential in a long-term agricultural experiment. To identify potential differences in microbial taxonomy and functionality, we generated six soil metagenomes of conventional (CT) and reduced (RT) tillage-treated topsoil samples, which differed in their potential extracellular cellulolytic activity as well as microbial biomass. Taxonomic analysis of metagenomic data revealed few differences between RT and CT and a dominance of Proteobacteria and Actinobacteria, whereas eukaryotic phyla were not prevalent. Prediction of cellulolytic enzymes revealed glycoside hydrolase families 1, 3, 5, 94, auxiliary activity family 8 and carbohydrate binding module 2 as the most abundant in soil. These were annotated mainly to the phyla of Proteobacteria, Actinobacteria and Bacteroidetes. These results suggest that the observed higher cellulolytic activity in RT soils can be explained by a higher microbial biomass or changed expression levels but not by shifts in the soil microbiome. Overall this study reveals stability of soil microbial communities and cellulolytic gene composition under the investigated tillage treatments.
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