Exploring the diversity of myxobacteria in a soil niche by myxobacteria-specific primers and probes

Bioprospecting of extremophilic perchlorate-reducing bacteria: report of promising Bacillus spp. isolated from sediments of the bay of Cartagena, Colombia

Three extremophile bacterial strains (BBCOL-009, BBCOL-014 and BBCOL-015), capable of degrading high concentrations of perchlorate at a range of pH (6.5 to 10.0), were isolated from Colombian Caribbean Coast sediments. Morphological features included Gram negative strain bacilli with sizes averaged of 1.75 × 0.95, 2.32 × 0.65 and 3.08 × 0.70 μm, respectively. The reported strains tolerate a wide range of pH (6.5 to 10.0); concentrations of NaCl (3.5 to 7.5% w/v) and KClO4- (250 to 10000 mg/L), reduction of KClO4- from 10 to 25%. LB broth with NaCl (3.5-30% w/v) and KClO4- (250-10000 mg/L) were used in independent trials to evaluate susceptibility to salinity and perchlorate, respectively. Isolates increased their biomass at 7.5 % (w/v) NaCl with optimal development at 3.5 % NaCl. Subsequently, ClO4- reduction was assessed using LB medium with 3.5% NaCl and 10000 mg/L ClO4-. BBCOL-009, BBCOL-014 and BBCOL-015 achieved 10%, 17%, and 25% reduction of ClO4-, respectively. The 16 S rRNA gene sequence grouped them as Bacillus flexus T6186-2, Bacillus marisflavi TF-11 (T), and Bacillus vietnamensis 15 - 1 (T) respectively, with < 97.5% homology. In addition, antimicrobial resistance to ertapenem, vancomycine, amoxicillin clavulanate, penicillin, and erythromycin was present in all the isolates, indicating their high adaptability to stressful environments. The isolated strains from marine sediments in Cartagena Bay, Colombia are suitable candidates to reduce perchlorate contamination in different environments. Although the primary focus of the study of perchlorate-reducing and resistant bacteria is in the ecological and agricultural realms, from an astrobiological perspective, perchlorate-resistant bacteria serve as models for astrobiological investigations.

Mining the soil myxobacteria and finding sources of anti-diabetic metabolites

Secondary metabolites produced by myxobacterial genera are often characterized as diverse molecules with unique structural properties which drove us to search for myxobacterial source of anti-diabetic drug discovery. In the present study, from 80 soil samples, out of sixty-five observed isolates, 30 and 16 were purified as Myxococcus and non-Myxococcus, respectively. Isolated strains taxonomically belonged to the genera Myxococcus, Corallococcus and Cystobacter, Archangium, Nanocystis, and Sorangium, and some could not be attributed. Secondary metabolites of selected non-Myxococcus isolates extracted by the liquid-liquid method showed that the myxobacterium UTMC 4530 demonstrated the highest inhibition on the formation of carbonyl group and fructosamine, respectively. In addition, it showed 23% and 15.8% inhibitory activity on α-glucosides and α-amylase compared to acarbose (23%, 18%), respectively. The extract of strain UTMC 4530 showed 35% induction effect on glucose adsorption while showing no radical scavenging activity and no toxic effect on HRBC lysis and HepG2 in cytotoxicity assays. The strain UTMC 4530 (ON808962), with the multiple antidiabetic activity, showed 87.3% similarity to Corallococcus llansteffanensis which indicates its affiliation to a new genus. The results of this study revealed that secondary metabolites produced by strain UTMC 4530 can be considered a promising source to find new therapeutic and pharmaceutical applications perhaps a multi-mechanism anti-diabetic compound.

Impacts of high-quality coal mine drainage recycling for replenishment of aquatic ecosystems in arid regions of China: Bacterial community responses

Coal mine water is usually recycled as supplementary water for aquatic ecosystems in arid and semiarid mining regions of China. To ensure ecosystem health, the coal mine water is rigorously treated using several processes, including reverse osmosis, to meet surface water quality standards. However, the potential environmental impacts of this management pattern on the ecological function of receiving water bodies are unclear. In this study, we built several microcosm water ecosystems to simulate the receiving water bodies. High-quality treated coal mine drainage was mixed into the model water bodies at different concentrations, and the sediment bacterial community response and functional changes were systematically investigated. The results showed that the high-quality coal mine drainage could still shape bacterial taxonomic diversity, community composition and structure, with a concentration threshold of approximately 50%. Moreover, both the Mantel test and the structural equation model indicated that the salinity fluctuation caused by the receiving of coal mine drainage was the primary factor shaping the bacterial communities. 10 core taxa in the molecular ecological network influenced by coal mine drainage were identified, with the most critical taxa being patescibacteria and g_Geothermobacter. Furthermore, the pathway of carbohydrate metabolism as well as signaling molecules and interactions was up-regulated, whereas amino acid metabolism showed the opposite trend. All results suggested that the complex physical-chemical and biochemical processes in water ecosystems may be affected by the coal mine drainage. The bacterial community response and underlying functional changes may accelerate internal nutrient cycling, which may have a potential impact on algal bloom outbreaks.

Diversity of Myxobacteria Isolated from Indonesian Mangroves and Their Potential for New Antimicrobial Sources

Mangroves are unique intertidal ecosystems that provide ecological niches to different microbes, which play various roles in nutrient recycling and diverse environmental activities. The association between myxobacteria and mangroves are hitherto poorly understood. The aim of our study was to evaluate the myxobacterial community composition as well as isolate myxobacteria and to characterize the antimicrobial activity of myxobacteria isolates from Indonesian mangroves. Twenty-five cultivable myxobacteria were affiliated in six genera: Myxococcus, Corallococcus, Archangium, Chondromyces, Racemicystis and Nannocystis of the order Myxococcales based on partial 16S rRNA gene sequences. Thirteen crude extracts showed moderate activities against at least one of human pathogenic microorganisms. The crude extract of Racemicystis sp. strain 503MSO indicated a novel compound, which has not been reported in the database yet and the identification of this compound needs further study. The myxobacterial communities of three different sampling sites were analyzed using primers adapted for the myxobacteria group identification. The results showed that myxobacterial communities are more diverse than assumed. Therefore, our study has highlighted the importance of the mangrove habitat as promising harbor of myxobacteria as well as novel antimicrobial compounds with activity against pathogenic microorganisms.

Two new Polyangium species, P. aurulentum sp. nov. and P. jinanense sp. nov., isolated from a soil sample

Polyangium belongs to Polyangiaceae family of Myxococcales, a taxonomic group well-known for their extraordinary social lifestyle and diverse novel gene clusters of secondary metabolites. A yellow-golden strain, designated SDU3-1^T, and two rose pink strains, designated SDU13 and SDU14^T, were isolated from a soil sample. These three strains were aerobic, mesophilic, not salt-tolerant and were able to prey on living microorganisms. SDU13 and SDU14^T formed solitary sporangioles under starvation conditions, while SDU3-1^T had no fruiting body structures. They showed 95.9-97.0% (SDU3-1^T) or 98.7-98.9% (SDU13 and SDU14^T) 16S rRNA gene similarity with the type strains of Polyangium, but were phylogenetically separate from them based on the 16S rRNA gene and genome sequences. Their genomes were 12.3 Mbp (SDU3-1^T), 13.9 Mbp (SDU13) and 13.8 Mbp (SDU14^T) with the G + C content range of 68.3-69.4 mol%. The average nucleotide identity and DNA-DNA hybridization analyses of genomes further indicated that these three strains belonged to two new species in Polyangium. Their major fatty acids were C_18:1ω9c, C_16:0 and C_18:0. The polyphasic taxonomic characterization suggest that the three strains represent two novel species in the genus Polyangium, for which the names Polyangium aurulentum sp. nov. and Polyangium jinanense sp. nov. are proposed, and the type strains are SDU3-1^T (=CGMCC 1.16875^T = KCTC 72136^T) and SDU14^T (=CCTCC AB 2021123^T = KCTC 82625^T), respectively.

Myxobacteria as a Source of New Bioactive Compounds: A Perspective Study

Myxobacteria are unicellular, Gram-negative, soil-dwelling, gliding bacteria that belong to class δ-proteobacteria and order Myxococcales. They grow and proliferate by transverse fission under normal conditions, but form fruiting bodies which contain myxospores during unfavorable conditions. In view of the escalating problem of antibiotic resistance among disease-causing pathogens, it becomes mandatory to search for new antibiotics effective against such pathogens from natural sources. Among the different approaches, Myxobacteria, having a rich armor of secondary metabolites, preferably derivatives of polyketide synthases (PKSs) along with non-ribosomal peptide synthases (NRPSs) and their hybrids, are currently being explored as producers of new antibiotics. The Myxobacterial species are functionally characterized to assess their ability to produce antibacterial, antifungal, anticancer, antimalarial, immunosuppressive, cytotoxic and antioxidative bioactive compounds. In our study, we have found their compounds to be effective against a wide range of pathogens associated with the concurrence of different infectious diseases.

Global Geographic Diversity and Distribution of the Myxobacteria

Bacteria are globally distributed in various environments on earth, but a global view of the geographic diversity and distribution of a single taxon is lacking. The Earth Microbiome Project (EMP) has established a global collection of microbial communities, providing the possibility for such a survey. Myxococcales is a bacterial order with a potent ability to produce diverse natural products and have wide application potential in agriculture, biomedicine, and environmental protection. In this study, through a comparative analysis of the EMP data and public information, we determined that myxobacteria account for 2.34% of the total bacterial operational taxonomic units (OTUs), and are one of the most diverse bacterial groups on Earth. Myxococcales OTUs are globally distributed and prefer nonsaline soil and sediments, followed by saline environments, but rarely appear in host-associated environments. Myxobacteria are among the least-investigated bacterial groups. The presently cultured and genome-sequenced myxobacteria are most likely environmentally widespread and abundant taxa, and account for approximately 10% and 7% of the myxobacterial community (>97% similarity), respectively. This global panoramic view of the geographic distribution and diversity of myxobacteria, as well as their cultured and genome-sequenced information, will enable us to explore these important bioresources more reasonably and efficiently. The diversity and distribution of myxobacteria beyond the EMP data are further discussed.

IMPORTANCE 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. The ecological importance of myxobacteria in major ecosystems is becoming established, but the global geographic diversity and distribution remain unclear. From a global survey we revealed that Myxococcales OTUs are globally distributed and prefer nonsaline soil and sediments, followed by saline environments, but rarely appear in host-associated environments. The global panoramic view of the geographic distribution and diversity of myxobacteria, as well as their cultured and genome-sequenced information, will enable us to explore these important bioresources more reasonably and efficiently.

Both Soil Bacteria and Soil Chemical Property Affected the Micropredator Myxobacterial Community: Evidence from Natural Forest Soil and Greenhouse Rhizosphere Soil

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. Here we hypothesize the regulation of bacterial abundance and community composition on soil myxobacterial community. Field investigation indicated that the relative abundance of Myxococcales in subtropical and tropical forest soil from South China was 1.49-4.74% of all the 16S rRNA gene sequences, and myxobacterial community composition differed between subtropical and tropical forest. The canonical correspondence analysis and variation partitioning analysis indicated that biotic factor (bacterial community composition) showed slightly stronger explanation for variation of myxobacteria than soil properties (soil pH and soil organic matter). Based on the rhizosphere bacterial network, the greenhouse mesocosm experiment showed that most of the myxobacterial links were with Gram-negative bacteria, except that some nodes from Haliangiacea and Polyangiaceae interacted with actinomycetes and actinomycetes-like Gram-positive bacteria. We inferred that myxobacteria preferential predation on specific bacterial taxa may explain the influence of bacteria on myxobacterial community. Further study confirming the biological process of myxobacterial predation in situ is necessary to advance the understanding of the ecological role of predation behavior in the microbial world.

Biodegradation of biodiesel-oil by Cellulosimicrobium sp. Isolated from Colombian Caribbean soils

Biodiesel is considered to be a natural substitute for fossil fuel. The comparatively low toxicity of biodiesel and its susceptibility to microbial biodegradation could reduce its environmental impact. Currently, biodiesel is sold previously mixed with petroleum-based hydrocarbons. The aim of this work was to measure the biodegradation potential of commercially available biodiesel, using bacterial strains (BBCOL-001, BBCOL-002, and BBCOL-003) isolated from a tropical forest soils in the Colombian Caribbean. According to nucleotide sequencing of the gene encoding for 16S rRNA, the strains belong to members of the genus Cellulosimicrobium. GC-MS analysis showed that biodiesel-oil alkanes were degraded by an average of 81.5% with optical density reaching 0.2-0.3 in minimal salt media at 37°C for 5 days. Individual diesel-oil alkanes were degraded by the strains at rates between 64.9% to 100%. The increase in bacterial biomass confirmed the use of the substrates by the microorganisms, suggesting these hydrocarbons are a carbon source. Changes in the biochemical behaviour of the strains suggested their capacity to adapt to environmental conditions might be an important resource for bioremediation.

Long-term nitrogen application decreases the abundance and copy number of predatory myxobacteria and alters the myxobacterial community structure in the soil

Myxobacteria are fascinating micro-predators due to their extraordinary social lifestyle, which is unique in the bacterial domain. These taxa are metabolically active in the soil microbial food web and control populations of soil microbes. However, the effects of fertilisation treatments on predatory myxobacteria in agricultural systems are often overlooked. Here, the high-throughput absolute abundance quantification (HAAQ) method was employed to investigate the abundance and cell density of myxobacteria in the Red Soil Experimental Station fields following 29 years of fertilisation. Using 16S rRNA gene amplicons, we detected a total of 419 myxobacterial operational taxonomic units (OTUs), accounting for 0.25-2.70% of the total bacterial abundance. Significantly different myxobacterial communities were found between nitrogen-fertilised (N_cluster) and manure-fertilised (M_cluster) samples by principal coordinate analysis (PCoA), analysis of similarities (ANOSIM), and Manhattan analysis (p < 0.05). N fertiliser treatments significantly decreased the myxobacterial abundance and copy number, species accumulation index (S), and Shannon index (p < 0.05). Furthermore, UpSet plots showed that the OTU number in the N fertiliser treatment was only 24.4% of that in the M treatment, as the application of N decreased the number of low-abundance myxobacterial OTUs. In addition, network analysis, redundancy analysis (RDA), and random forest (RF) analysis showed that myxobacterial abundance and copy number were the most important variables predicting the soil bacterial community and functional gene α- and β-diversity (P < 0.05). Our findings imply that soil acidification caused by the application of nitrogen fertilisers is the most important driver of the decrease in the myxobacterial abundance and copy number in the soil. We suggest that the changes in the abundance and number of myxobacteria are strongly correlated with the overall bacterial α- and β-diversity indices. In addition, such changes may be an important factor in the overall changes in microbial communities.

Meta-16S rRNA Gene Phylogenetic Reconstruction Reveals the Astonishing Diversity of Cosmopolitan Myxobacteria

Numerous ecological studies on myxobacteria have been conducted, but their true diversity remains largely unknown. To bridge this gap, we implemented a comprehensive survey of diversity and distribution of myxobacteria by using 4997 publicly available 16S rRNA gene sequences (≥1200 bp) collected from several hundred sites across multiple countries and regions. In this study, the meta-16S rRNA gene phylogenetic reconstruction clearly revealed that these sequences could be classified into 998 species, 445 genera, 58 families, and 20 suborders, the great majority of which belonged to new taxa. Most cultured myxobacteria were strongly inclined to locate on the shallow branches of the phylogenetic tree; on the contrary, the majority of uncultured myxobacteria located on the deep branches. The geographical analysis of sequences based on their environmental categories clearly demonstrated that myxobacteria show a nearly cosmopolitan distribution, despite the presence of some habitat-specific taxa, especially at the genus and species levels. Among the abundant suborders, Suborder_4, Suborder_15, and Suborder_17 were more widely distributed in marine environments, while the remaining suborders preferred to reside in terrestrial ecosystems. In conclusion, this study profiles a clear framework of diversity and distribution of cosmopolitan myxobacteria and sheds light on the isolation of uncultured myxobacteria.

Perchlorate-Reducing Bacteria from Hypersaline Soils of the Colombian Caribbean

Perchlorate (ClO₄ ^-) has several industrial applications and is frequently detected in environmental matrices at relevant concentrations to human health. Currently, perchlorate-degrading bacteria are promising strategies for bioremediation in polluted sites. The aim of this study was to isolate and characterize halophilic bacteria with the potential for perchlorate reduction. Ten bacterial strains were isolated from soils of Galerazamba-Bolivar, Manaure-Guajira, and Salamanca Island-Magdalena, Colombia. Isolates grew at concentrations up to 30% sodium chloride. The isolates tolerated pH variations ranging from 6.5 to 12.0 and perchlorate concentrations up to 10000 mg/L. Perchlorate was degraded by these bacteria on percentages between 25 and 10. 16S rRNA gene sequence analysis indicated that the strains were phylogenetically related to Vibrio, Bacillus, Salinovibrio, Staphylococcus, and Nesiotobacter genera. In conclusion, halophilic-isolated bacteria from hypersaline soils of the Colombian Caribbean are promising resources for the bioremediation of perchlorate contamination.

Simulacricoccus ruber gen. nov., sp. nov., a microaerotolerant, non-fruiting, myxospore-forming soil myxobacterium and emended description of the family Myxococcaceae

A non-fruiting group of myxobacteria was previously speculated to exist in nature based on metagenomics data containing uncultured members of the order Myxococcales. Here, we describe a myxobacterial strain, designated MCy10636^T, which was isolated from a German soil sample collected in 2013. It exhibits swarming characteristics but atypically produces myxospores in the absence of fruiting bodies. The novel strain stains Gram-negative and Congo-red-negative and is characterized mesophilic, neutrophilic, chemoheterotrophic and microaerotolerant. Branched-chain fatty acids are the predominant cellular fatty acids over the straight-chain type, and contain the major fatty acids iso-C17 : 0 2-OH, C16 : 1, iso-C17 : 0 and iso-C15 : 0. Based on blastn results, the 16S rRNA gene sequence reveals similarity (97 %) to Aggregicoccus edonensis MCy1366^T, (97 %) Myxococcus macrosporus DSM 14697^T, (96 %) Corallococcus coralloides DSM2259^T and Corallococcus exiguus Cc e167^T. Phylogenetic analysis showed a novel lineage of MCy10636^T in the family Myxococcaceae, suborder Cystobacterineae. Based on polyphasic taxonomic characterization, we propose that this unusual, non-fruiting, myxospore-forming and microaerotolerant myxobacterial strain, MCy10636^T, represents a novel genus and species, Simulacricoccus ruber gen. nov., sp. nov. (DSM 106554^T=NCCB 100651^T).

Diversity of Myxobacteria-We Only See the Tip of the Iceberg

The discovery of new antibiotics is mandatory with regard to the increasing number of resistant pathogens. One approach is the search for new antibiotic producers in nature. Among actinomycetes, Bacillus species, and fungi, myxobacteria have been a rich source for bioactive secondary metabolites for decades. To date, about 600 substances could be described, many of them with antibacterial, antifungal, or cytostatic activity. But, recent cultivation-independent studies on marine, terrestrial, or uncommon habitats unequivocally demonstrate that the number of uncultured myxobacteria is much higher than would be expected from the number of cultivated strains. Although several highly promising myxobacterial taxa have been identified recently, this so-called Great Plate Count Anomaly must be overcome to get broader access to new secondary metabolite producers. In the last years it turned out that especially new species, genera, and families of myxobacteria are promising sources for new bioactive metabolites. Therefore, the cultivation of the hitherto uncultivable ones is our biggest challenge.

Myxobacteria in high moor and fen: An astonishing diversity in a neglected extreme habitat

Increasing antibiotic resistances of numerous pathogens mean that myxobacteria, well known producers of new antibiotics, are becoming more and more interesting. More than 100 secondary metabolites, most of them with bioactivity, were described from the order Myxococcales. Especially new myxobacterial genera and species turned out to be reliable sources for novel antibiotics and can be isolated from uncommon neglected habitats like, for example, acidic soils. Almost nothing is known about the diversity of myxobacteria in moors, except some information from cultivation studies of the 1970s. Therefore, we evaluated the myxobacterial community composition of acidic high moor and fen both with cultivation‐independent 16S rRNA clone bank analysis and with cultivation. Phylogenetic analyses of clone sequences revealed a great potential of undescribed myxobacteria in high moor and fen, whereby all sequences represent unknown taxa and were detected exclusively by cultivation‐independent analyses. However, many clones were assigned to sequences from other cultivation‐independent studies of eubacterial diversity in acidic habitats. Cultivation revealed different strains exclusively from the genus Corallococcus. Our study shows that the neglected habitat moor is a promising source and of high interest with regard to the cultivation of prospective new bioactive secondary metabolite producing myxobacteria.

Self-identity reprogrammed by a single residue switch in a cell surface receptor of a social bacterium

The ability to recognize close kin confers survival benefits on single-celled microbes that live in complex and changing environments. Microbial kinship detection relies on perceptible cues that reflect relatedness between individuals, although the mechanisms underlying recognition in natural populations remain poorly understood. In myxobacteria, cells identify related individuals through a polymorphic cell surface receptor, TraA. Recognition of compatible receptors leads to outer membrane exchange among clonemates and fitness consequences. Here, we investigated how a single receptor creates a diversity in recognition across myxobacterial populations. We first show that TraA requires its partner protein TraB to function in cell-cell adhesion. Recognition is shown to be traA allele-specific, where polymorphisms within TraA dictate binding selectivity. We reveal the malleability of TraA recognition, and seemingly minor changes to its variable region reprogram recognition outcomes. Strikingly, we identify a single residue (A/P205) as a molecular switch for TraA recognition. Substitutions at this position change the specificity of a diverse panel of environmental TraA receptors. In addition, we engineered a receptor with unique specificity by simply creating an A205P substitution, suggesting that modest changes in TraA can lead to diversification of new recognition groups in nature. We hypothesize that the malleable property of TraA has allowed it to evolve and create social barriers between myxobacterial populations and in turn avoid adverse interactions with relatives.

Comparison of myxobacterial diversity and evaluation of isolation success in two niches: Kiritimati Island and German compost

Myxobacteria harbor an enormous potential for new bioactive secondary metabolites and therefore the isolation of in particular new groups is of great interest. The diversity of myxobacteria present in two ecological habitats, namely sand from Kiritimati Island and German compost, was evaluated by both cultivation‐based and cultivation‐independent methods. Phylogenetic analyses of the strains in comparison with 16S rRNA gene sequences from cultured and uncultured material in GenBank revealed a great potential of undescribed myxobacteria in both sampling sites. Several OTUs (operational taxonomic units) represent unknown taxa and were detected by clone bank analyses, but not by cultivation. Clone bank analyses indicated that the myxobacterial community is predominantly indigenous. The 16S rDNA libraries from the two samples were generated from total community DNA with myxobacterial specific forward and universal reverse primer sets. The clones were partially sequenced. Cultivation was successful for exclusively bacteriolytic, but not for cellulolytic myxobacteria and revealed 42 strains from the genera Corallococcus, Myxococcus, and Polyangium. The genera of Myxococcaceae family were represented by both approaches. But, even in this well studied family, as well as in the suborders Sorangiineae and Nannocystineae, a considerable number of clones were assigned to, if any, uncultivated organisms. Our study shows an overrepresentation of the genera Myxococcus spp. and Corallococcus spp. with standard cultivation methods. However, high deficits are demonstrated in the cultivation success of the myxobacterial diversity detected by exclusively cultivation‐independent approaches. Especially, clades which are exclusively represented by clones are of high interest with regard to the cultivation of new bioactive secondary metabolite producers.

How Myxobacteria Cooperate

Prokaryotes often reside in groups where a high degree of relatedness has allowed the evolution of cooperative behaviors. However, very few bacteria or archaea have made the successful transition from unicellular to obligate multicellular life. A notable exception is the myxobacteria, in which cells cooperate to perform group functions highlighted by fruiting body development, an obligate multicellular function. Like all multicellular organisms, myxobacteria face challenges in how to organize and maintain multicellularity. These challenges include maintaining population homeostasis, carrying out tissue repair and regulating the behavior of non-cooperators. Here, we describe the major cooperative behaviors that myxobacteria use: motility, predation and development. In addition, this review emphasizes recent discoveries in the social behavior of outer membrane exchange, wherein kin share outer membrane contents. Finally, we review evidence that outer membrane exchange may be involved in regulating population homeostasis, thus serving as a social tool for myxobacteria to make the cyclic transitions from unicellular to multicellular states.

Exploring the diversity of Acinetobacter populations in river water with genus-specific primers and probes

This study aimed to explore the diversity of river water Acinetobacter populations using culture-dependent and -independent methods. Pyrosequencing indicated that 1.5% of the total sequences from Qiandeng River water were classified as Acinetobacter. Twelve Acinetobacter strains were isolated from three different sampling sites of the Qiandeng River. Based on culture-dependent methods, A. johnsonii, A. lwoffii and A. guillouiae were the most abundantly represented Acinetobacter strains among the upper, middle and downstream populations of the river. Probing of three Acinetobacter-enriched 16S rRNA gene libraries with the Acinetobacter specific probe Act660F revealed 42 unique 16S rRNA gene sequences exhibiting a similarity of 94.9-99.9% with the known Acinetobacter strains. Among the uncultured Acinetobacter sequences, 50%, 58.3% and 68.8% of those obtained from upstream sampling site A, middle stream sampling site B and downstream sampling site C were phylogenetically located within Group I. This Group represented the most abundant strains of Acinetobacter populations in river water based on culture-independent methods. The results indicated that culture-independent methods provide more detailed information on the diversity of Acinetobacter populations than that based on culture-dependent methods. Therefore, the development of new and efficient isolation methods to identify uncultured Acinetobacter species is required.

Approach to analyze the diversity of myxobacteria in soil by semi-nested PCR-denaturing gradient gel electrophoresis (DGGE) based on taxon-specific gene

The genotypic diversity of insoluble macromolecules degraded myxobacteria, provided an opportunity to discover new bacterial resources and find new ecological functions. In this study, we developed a semi-nested-PCR-denaturing gradient gel electrophoresis (DGGE) strategy to determine the presence and genotypic diversity of myxobacteria in soil. After two rounds of PCR with myxobacteria-specific primers, an 194 bp fragment of mglA, a key gene involved in gliding motility, suitable for DGGE was obtained. A large number of bands were observed in DGGE patterns, indicating diverse myxobacteria inhabiting in soils. Furthermore, sequencing and BLAST revealed that most of the bands belonged to the myxobacteria-group, and only three of the twenty-eight bands belonged to other group, i.e., Deinococcus maricopensis. The results verified that myxobacterial strains with discrepant sequence compositions of gene mglA could be discriminated by DGGE with myxobacteria-specific primers. Collectively, the developed semi-nested-PCR-DGGE strategy is a useful tool for studying the diversity of myxobacteria.

Myxobacterial community is a predominant and highly diverse bacterial group in soil niches

Although many molecular ecological surveys have been conducted, there is little concerning the details of specific bacterial groups, resulting in an incomplete understanding of the microorganismal composition and community structures in the environment. Myxobacteria are micropredators that are metabolically active in the soil microbial food web and have typically been considered minority components of soil bacterial communities. In this study, we surveyed the percentage of myxobacteria in a single soil sample via pyrosequencing on combined universal libraries of the V3-V4 and V6-V8 hypervariable regions of the 16S rRNA gene. Surprisingly, myxobacteria accounted for 4.10% of the bacterial community and 7.5% of the total operational taxonomic units at the 3% similarity level in the soil, containing almost all of the cultivated myxobacterial families or genera. To testify the appearance of myxobacteria in soil niches, we retrieved myxobacteria-related 16S rRNA gene sequences of 103 high-throughput sequencing data sets obtained from public databases. The results indicated that myxobacteria-related sequences were among the predominant groups in these data sets accounting for 0.4-4.5% of bacterial communities. The abundance of myxobacterial communities were correlated with site temperature, carbon-to-nitrogen ratio and pH values. Based on these results, we discussed the survival strategies of myxobacterial community in soil.

Diversity of epothilone producers among Sorangium strains in producer-positive soil habitats

Large-scale surveys show that the anti-tumour compounds known as epothilones are produced by only a small proportion of Sorangium strains, thereby greatly hampering the research and development of these valuable compounds. In this study, to investigate the niche diversity of epothilone-producing Sorangium strains, we re-surveyed four soil samples where epothilone producers were previously found. Compared with the < 2.5% positive strains collected from different places, epothilone producers comprised 25.0-75.0% of the Sorangium isolates in these four positive soil samples. These sympatric epothilone producers differed not only in their 16S rRNA gene sequences and morphologies but also in their production of epothilones and biosynthesis genes. A further exploration of 14 soil samples collected from a larger area around a positive site showed a similar high positive ratio of epothilone producers among the Sorangium isolates. The present results suggest that, in an area containing epothilone producers, the long-term genetic variations and refinements resulting from selective pressure form a large reservoir of epothilone-producing Sorangium strains with diverse genetic compositions.

Molecular recognition in myxobacterial outer membrane exchange: functional, social and evolutionary implications

Through cooperative interactions, bacteria can build multicellular communities. To ensure that productive interactions occur, bacteria must recognize their neighbours and respond accordingly. Molecular recognition between cells is thus a fundamental behaviour, and in bacteria important discoveries have been made. This MicroReview focuses on a recently described recognition system in myxobacteria that is governed by a polymorphic cell surface receptor called TraA. TraA regulates outer membrane exchange (OME), whereby myxobacterial cells transiently fuse their OMs to efficiently transfer proteins and lipids between cells. Unlike other transport systems, OME is rather indiscriminate in what OM goods are transferred. In contrast, the recognition of partnering cells is discriminatory and only occurs between cells that bear identical or closely related TraA proteins. Therefore TraA functions in kin recognition and, in turn, OME helps regulate social interactions between myxobacteria. Here, I discuss and speculate on the social and evolutionary implications of OME and suggest it helps to guide their transition from free-living cells into coherent and functional populations.

Isolation and identification of myxobacteria from saline-alkaline soils in Xinjiang, China

Fifty-eight terrestrial and salt-tolerant myxobacteria were isolated from the saline-alkaline soils collected from Xinjiang, China. Based on the morphologies and the 16S rRNA gene sequences, these isolates were assigned into 6 genera, Myxococcus, Cystobacter, Corallococcus, Sorangium, Nannocystis and Polyangium. All the strains grew better with 1% NaCl than without NaCl. Some Myxococcus strains were able to grow at 2% NaCl concentration, suggesting that these strains may be particular type of terrestrial myxobacteria.

The existence and diversity of myxobacteria in lake mud - a previously unexplored myxobacteria habitat

Myxobacteria are widely distributed in soil and oceanic sediment with a phylogeographic separation at high levels of classification. However, it is unclear whether freshwater environments, from which there has been no isolation report of myxobacteria since 1981, are habitats for myxobacteria. In this study, we investigated the presence of myxobacteria in lake mud using a two-step strategy. First, we constructed two universal bacterial libraries from the V3-V4 (V34) and V6-V8 (V678) hypervariable regions of 16S rRNA gene sequences. High-throughput 454 pyrosequencing revealed that myxobacteria were one of the major bacterial groups in the lake mud. They accounted for 5.77% of the total sequences and 7.52% of the total operational taxonomic units (OTUs) at a phylogenetic distance of 0.03. The community composition and taxonomic structure of the mud myxobacterial community were further analysed using myxobacteria-enriched libraries targeting the V34 and V678 regions, which were amplified with Cystobacterineae- and Sorangineae-specific primer pairs respectively. Phylogenetic analysis showed that the limnetic myxobacteria exhibited closer relationships to their soil than their marine relatives, but there were also exclusive taxa of limnetic myxobacteria detected. These results, together with a survey on available GenBank data, indicate that lake mud is a primary habitat for myxobacteria.

Expanded phylogeny of myxobacteria and evidence for cultivation of the 'unculturables'

An expanded neighbour-joining tree of myxobacteria is presented based on the analysis of 16S rRNA gene sequences of 101 strains (including types) representing 3 suborders, 6 families, 20 genera, 46 species, and 12 other novel taxa. The distinctions amongst members of the three suborders (Sorangiineae, Cytobacterineae and Nannocystineae) are reaffirmed. The positions of anaerobic myxobacteria, novel groups (Pyxidicoccus and several Cystobacter species) in Cystobacterineae, the marine genera (Plesiocystis, Haliangium, Enhygromyxa), and two additional novel taxa ('Paraliomyxa miuraensis', brackish-water isolate) were together revealed for the first time. Changes in the nomenclature of several isolates (Polyangium vitellinum Pl vt1(T), Polyangium thaxteri Pl t3, Polyangium cellulosum, NOSO-1, NOCB-2, NOCB-4) are also highlighted. Suborders Sorangiineae and Nannocystineae hold great promise for novel strain discovery. In Sorangiineae, the new family Phaselicystidaceae, with a monotypic genus, was added. Nine additional novel taxa were discovered in this suborder for which new genera or even families may be erected in the near future. These taxa appear to represent the so-called viable but not culturable (VBNC) group of myxobacteria. Based on at least 4% phylogenetic distance, new clades were formed comprising of novel Nannocystineae and Sorangiineae isolates. Overall, the myxobacteria, on the basis of bracket distance, could be divided into 16 clusters, as supported by tree topology and a morphology-based approach.

Interspecies chemical communication in bacterial development

Our view of bacteria, from the earliest observations through the heyday of antibiotic discovery, has shifted dramatically. We recognize communities of bacteria as integral and functionally important components of diverse habitats, ranging from soil collectives to the human microbiome. To function as productive communities, bacteria coordinate metabolic functions, often requiring shifts in growth and development. The hallmark of cellular development, which we characterize as physiological change in response to environmental stimuli, is a defining feature of many bacterial interspecies interactions. Bacterial communities rely on chemical exchanges to provide the cues for developmental change. Traditional methods in microbiology focus on isolation and characterization of bacteria in monoculture, separating the organisms from the surroundings in which interspecies chemical communication has relevance. Developing multispecies experimental systems that incorporate knowledge of bacterial physiology and metabolism with insights from biodiversity and metagenomics shows great promise for understanding interspecies chemical communication in the microbial world.

Fruiting and non-fruiting myxobacteria: A phylogenetic perspective of cultured and uncultured members of this group

The diversity of myxobacteria present in campus garden soil was surveyed by both cultivation-based and cultivation-independent methods. Detailed phylogenetic analysis of cultured and uncultured myxobacteria 16S rRNA gene sequences revealed that many undescribed relatives of the myxobacteria exist in nature. Molecular systematic analyses also revealed that myxobacterial genera described to date on the basis of the morphology of multi-cellular fruiting bodies were mostly monophyletic. However, these known taxa comprised only in a small part of the sequences recovered directly from soil in a cultivation-independent approach, indicating that the group is much more diverse than previously thought. We propose that the myxobacteria exist in two forms: the fruiting and the non-fruiting types. Most of the uncultured myxobacteria may represent taxa which rarely form fruiting bodies, or may lack some or all of the developmental genes needed for fruiting body formation. In order to identify non-fruiting myxobacteria, new morphology-independent cultivation and isolation techniques need to be developed.