Group Of Actinobacteria Research Articles

Genome editing in ubiquitous freshwater Actinobacteria.

To advance bioproduction or bioremediation in large, unsupervised environmental systems such as ponds, wastewater lagoons, or groundwater systems, it will be necessary to develop diverse genetically amenable microbial model organisms. Although we already genetically modify a few key species, tools for engineering more microbial taxa, with different natural phenotypes, will enable us to genetically engineer multispecies consortia or even complex communities. Developing genetic tools for modifying freshwater bacteria is particularly important, as wastewater, production ponds or raceways, and contaminated surface water are all freshwater systems where microbial communities are already deployed to do work, and the outputs could potentially be enhanced by genetic modifications. Here, we demonstrate that common tools for genome editing can be used to inactivate specific genes in two representatives of a very widespread, environmentally relevant group of Actinobacteria. These Actinobacteria are found in almost all tested surface freshwater environments, where they co-occur with primary producers, and genome-editing tools in these species are thus a step on the way to engineering microbial consortia in freshwater environments.

Volatile communication in Actinobacteria: a language for secondary metabolism regulation

BackgroundVolatile compounds are key elements in the interaction and communication between organisms at both interspecific and intraspecific levels. In complex bacterial communities, the emission of these fast-acting chemical messengers allows an exchange of information even at a certain distance that can cause different types of responses in the receiving organisms. The changes in secondary metabolism as a consequence of this interaction arouse great interest in the field of searching for bioactive compounds since they can be used as a tool to activate silenced metabolic pathways. Regarding the great metabolic potential that the Actinobacteria group presents in the production of compounds with attractive properties, we evaluated the reply the emitted volatile compounds can generate in other individuals of the same group.ResultsWe recently reported that volatile compounds released by different streptomycete species trigger the modulation of biosynthetic gene clusters in Streptomyces spp. which finally leads to the activation/repression of the production of secondary metabolites in the recipient strains. Here we present the application of this rationale in a broader bacterial community to evaluate volatiles as signaling effectors that drive the activation of biosynthesis of bioactive compounds in other members of the Actinobacteria group. Using cocultures of different actinobacteria (where only the volatile compounds reach the recipient strain) we were able to modify the bacterial secondary metabolism that drives overproduction (e.g., granaticins, actiphenol, chromomycins) and/or de novo production (e.g., collismycins, skyllamycins, cosmomycins) of compounds belonging to different chemical species that present important biological activities.ConclusionsThis work shows how the secondary metabolism of different Actinobacteria species can vary significantly when exposed in co-culture to the volatile compounds of other phylum-shared bacteria, these effects being variable depending on strains and culture media. This approach can be applied to the field of new drug discovery to increase the battery of bioactive compounds produced by bacteria that can potentially be used in treatments for humans and animals.

Compositional changes of dissolved organic molecules along water flow and their influencing factors in the Three Gorges Reservoir

Molecular composition of dissolved organic matter (DOM) and its influencing factors in river reservoirs remains elusive. Here, molecular compositions of DOM, bacterial community structures, and water physiochemistry were investigated in the field and microcosm samples of the Three Gorges Reservoir (TGR). The results showed that DOM molecular compositions were significantly (R2 = 0.245, p < 0.001) correlated with bacterial community structures in the studied field samples, suggesting that bacteria may actively interact with DOM molecules. The molecular compositions of DOM in the studied field samples were significantly (p < 0.05) affected by the distance between the sample sites and the Three Gorges Dam and by bacterial groups of Actinobacteria and Alphaproteobacteria, suggesting that both hydrological and bacterial processes may contribute to the variation in DOM molecular composition in the TGR water. Furthermore, microcosm experiments demonstrated that both microbial and abiotic processes may transform and/or produce DOM in the TGR, thereby affecting DOM molecular composition. Microbial process increased the average aromaticity index and decreased the carbon number of DOM molecules with increasing incubation duration; whereas average oxygen number, double bond equivalent, and oxidation state of carbon of DOM molecules increased during the first 14 days of incubation and began to decrease thereafter. Taken together, this study expands our understanding of the impact of microbial process on the DOM molecular composition in reservoir ecosystems, and has great implications for carbon cycling in major rivers.

Lettuce Soil Microbiome Modulated by an L-α-Amino Acid-Based Biostimulant

Maintenance of soil health is of foremost importance to sustain and increase crop productivity, while meeting the demand of a rising global population. Soil microbiome is gaining increasing attention as a modulator of soil health. Microbial communities confer traits to the soil as a living organism, which functions holistically and conforms part of the plant holobiont, reassembling the human-gut axis. Novel strategies in biostimulant development advocate for modulation of the native soil microbiome and the reinforcement of microbial networking to outpace pathogen inclusion. Consequently, we hypothesize that Terramin® Pro may promotes beneficial microorganisms, depending on the native microbiota of soil, which would lead to an improvement of crop performance indicators. We proposed a soil microbiome-based approach to characterize the effect of an L-α-amino acid based biostimulant (Terramin® Pro) on resulting plant phenotypes in lettuce cultivars (Lactuca sativa L.) to address our hypothesis. First, product application promoted Actinobacteria group in assorted soils with different track of agronomic practices. Secondly, biostimulant application improved chlorophyll content in particular soils deviating from standard conditions, i.e., sick or uncultivated ones. Specially, we observed that product application at 30 L ha−1 improved lettuce phenotype, while potentially promoted entomopathogenic fungi (Beauveria and Metarhizium spp.) and suppressed other lettuce disease-related fungi (Olpidium spp.) in nematode-infested soils. Further investigations could deepen into Terramin® Pro as a sustainable prebiotic strategy of soil indigenous microbiota, through in-house microbiome modulation, even in additional crops.

Characterization of three novel DyP-type peroxidases from Streptomyces chartreusis NRRL 3882.

Actinobacteria are known to produce extracellular enzymes including DyPs. We set out to identify and characterize novel peroxidases from Streptomyces chartreusis NRRL 3882, because S. chartreusis belongs to the small group of actinobacteria with three different DyPs. The genome of the actinomycete S. chartreusis NRRL 3882 was mined for novel DyP-type peroxidases. Three genes encoding for DyP-type peroxidases were cloned and overexpressed in Escherichia coli. Subsequent characterization of the recombinant proteins included examination of operating conditions such as pH, temperature and H2 O2 concentrations, as well as substrate spectrum. Despite their high sequence similarity, the enzymes named SCDYP1-SCDYP3 presented distinct preferences regarding their operating conditions. They showed great divergence in H2 O2 tolerance and stability, with SCDYP2 being most active at concentrations above 50 mmol l-1 . Moreover, SCDYP1 and SCDYP3 preferred acidic pH (typical for DyP-type peroxidases), whereas SCDYP2 was most active at pH8. Regarding the function of DyPs in nature, these results suggest that availability of different DyP variants with complementary activity profiles in one organism might convey evolutionary benefits. DyP-type peroxidases are able to degrade xenobiotic compounds and thus can be applied in biocatalysis and bioremediation. However, the native function of DyPs and the benefits for their producers largely remain to be elucidated.

Comprehensive genome analysis of Lentzea reveals repertoire of polymer-degrading enzymes and bioactive compounds with clinical relevance

The genus Lentzea is a rare group of actinobacteria having potential for the exploration of bioactive compounds. Despite its proven ability to produce compounds with medical relevance, Lentzea genome analysis remains unexplored. Here we show a detailed understanding of the genetic features, biosynthetic gene clusters (BGCs), and genetic clusters for carbohydrate-active enzymes present in the Lentzea genome. Our analysis determines the genes for core proteins, non-ribosomal peptide synthetase condensation domain, and polyketide synthases-ketide synthase domain. The antiSMASH-based sequence analysis identifies 692 BGCs among which 8% are identical to the BGCs that produce geosmin, citrulassin, achromosin (lassopeptide), vancosamine, anabaenopeptin NZ857/nostamide A, alkylresorcinol, BE-54017, and bezastatin. The remaining BGCs code for advanced category antimicrobials like calcium-dependent, glycosylated, terpenoids, lipopeptides, thiopeptide, lanthipeptide, lassopeptide, lingual antimicrobial peptide and lantibiotics together with antiviral, antibacterial, antifungal, antiparasitic, anticancer agents. About 28% of the BGCs, that codes for bioactive secondary metabolites, are exclusive in Lentzea and could lead to new compound discoveries. We also find 7121 genes that code for carbohydrate-degrading enzymes which could essentially convert a wide range of polymeric carbohydrates. Genome mining of such genus is very much useful to give scientific leads for experimental validation in the discovery of new-generation bioactive molecules of biotechnological importance.

Comparative genomics reveals broad genetic diversity, extensive recombination and nascent ecological adaptation in Micrococcus luteus

BackgroundMicrococcus luteus is a group of actinobacteria that is widely used in biotechnology and is being thought as an emerging nosocomial pathogen. With one of the smallest genomes of free-living actinobacteria, it is found in a wide range of environments, but intraspecies genetic diversity and adaptation strategies to various environments remain unclear. Here, comparative genomics, phylogenomics, and genome-wide association studies were used to investigate the genomic diversity, evolutionary history, and the potential ecological differentiation of the species.ResultsHigh-quality genomes of 66 M. luteus strains were downloaded from the NCBI GenBank database and core and pan-genome analysis revealed a considerable intraspecies heterogeneity. Phylogenomic analysis, gene content comparison, and average nucleotide identity calculation consistently indicated that the species has diverged into three well-differentiated clades. Population structure analysis further suggested the existence of an unknown ancestor or the fourth, yet unsampled, clade. Reconstruction of gene gain/loss events along the evolutionary history revealed both early events that contributed to the inter-clade divergence and recent events leading to the intra-clade diversity. We also found convincing evidence that recombination has played a key role in the evolutionary process of the species, with upto two-thirds of the core genes having been affected by recombination. Furthermore, distribution of mammal-associated strains (including pathogens) on the phylogenetic tree suggested that the last common ancestor had a free-living lifestyle, and a few recently diverged lineages have developed a mammal-associated lifestyle separately. Consistently, genome-wide association analysis revealed that mammal-associated strains from different lineages shared genes functionally relevant to the host-associated lifestyle, indicating a recent ecological adaption to the new host-associated habitats.ConclusionsThese results revealed high intraspecies genomic diversity of M. luteus and highlighted that gene gain/loss events and extensive recombination events played key roles in the genome evolution. Our study also indicated that, as a free-living species, some lineages have recently developed or are developing a mammal-associated lifestyle. This study provides insights into the mechanisms that drive the genome evolution and adaption to various environments of a bacterial species.

Biodiversity and biotechnological potential of marine derived actinobacteria from Black Sea coastal zone

Actinobacteria are economically and biotechnologically valuable prokaryotes. It is crucial that new group of actinobacteria from unexplored habitats, marine environmental conditions, will be pursued as sources of novel bioactive secondary metabolites. Therefore, actinobacterial strains were isolated from the Black Sea sediments and screened for production of antimicrobial metabolites and industrial enzymes. The isolates were identified with sequencing analysis by using 16S rDNA regions. Antimicrobial activity was determined by disc diffusion method by using extracts of fermentation broth inoculated with the isolates against seven pathogenic organisms. According to results, the majority of isolates belonged to Streptomyces genus. Their anticandidal activity and ability to produce cellulase enzyme were remarkable. In addition, it was determined that the isolates which not shown antimicrobial activity produced at least one industrial enzyme. As a result, the potential of isolates to be used as an antibiotic and enzyme producer in the industrial field is quite high.

Intensified 4-chlorophenol biodegradation in an aerobic sequencing batch reactor: Microbial and kinetic properties evaluation

In this paper, the microbial and biodegradation kinetics of acclimated-mixed sludge to 4-chlorophenol (4-CP) were investigated in an aerobic sequencing batch reactor (SBR). A molecular technique was applied to evaluate the bacterial variety and role in mixed biomass. Culture isolation and a 16S rDNA sequence authenticated the domination of Gram-positive high-G+C bacilli and coccobacilli with a 99% similarity belonging to the group of Actinobacteria. These isolates include Brevibacterium casei DSM20657, Corynebacterium callunae 10338, Microbacterium oxydan s XH0903, and Kocuria rhizophila Ag09. Those strains in the mixed condition aerobically removed 4-CP till a concentration of 800 mg L −1 . The biodegradation kinetics of 4-CP were adequately predicted by the Haldane formulae with a half-saturation constant ( K s ) and an inhibition constant ( K i ), of 9.12 and 609.7 mg L −1 , respectively. The maximum specific degradation rate ( q m ) was 20.33 mg 4-CP g −1 VSS h −1 . Amounts of the yield coefficient (Y) were among 0.25 and 0.48 mg VSS mg −1 COD. However, due to congregate of 5-chloro-2-hydroxymuconic semialdehyde (CHMS), an intermediate meta-cleavage product of 4-CP, the pure strains isolated from mixed sludge did not show a higher 4-CP-removal efficiency compared with the mixed sludge. Therefore, the use of mixed biomass in engineering systems has attracted increased attention for both environmental and biotechnological applications. • Representing firstly Gram positive high-G+C bacteria degrading 4-CP based on 16S rDNA. • Kinetic properties of acclimated-mixed sludge treating high concentration of 4-CP. • The Y value was observed to be from 0.25 to 0.48 mg VSS mg -1 COD. • The critical concentration of 4-CP and the K i /K s ratio were 74.5 mg L -1 and 66.85, respectively. • High concentration of 4-CP could be removed by SBR with acclimated-mixed sludge.

Rock varnish in La Proveedora/Sonora in the context of desert geobiological processes and landscape evolution

Desert varnish is a dark microlayer that forms on rocky surfaces that is usually associated with arid and desert environments. It consists mainly of clay minerals (60%), while the rest are Fe and Mn oxides. Growth rates are very slow and vary from <1 to 40 μm/ky. Although different proposals exist to explain their formation mechanisms, these processes are still unknown. Around the world, various groups and human communities have created petroglyphs with different meanings in desert varnish. In the Sonoran Desert, the archaeological site La Proveedora is known for having many petroglyphs made in granite rock varnishes. It is believed that people groups occupied the area during the mid-Holocene (ca 5000-3000 BC). The research was carried out by analyzing and looking for possible signals and contributions from past environments and current processes that are preserved in the varnish layers. The X-ray diffraction, laser breakdown spectra and scanning electron microscopy with energy dispersive spectroscopy analyses in varnish samples, showed that the distribution and concentrations of Fe and Mn exhibit an alternating behavior on a depth scale from the surface until contact with granite. The DNA analysis showed a major presence of the Proteobacteria and Actinobacteria groups. Notably, some of these microorganisms can incorporate Fe and Mn into their metabolic processes and mobilize them through the varnish for its formation. The 14C radiocarbon dating (370 ± 54 cal BP) indicates a very young age associated primarily with recent microorganisms. However, a first approximation was obtained for the minimum age (5000-1000 yr BP). The comparison between the areas of varnish and the surfaces within the petroglyphs suggests that the varnish formation occurred under conditions in the past when the humidity was higher, and that it is probably a very slow, intermittent or uncoated formation mechanism today.

Effects of wheat flour and culture period on bacterial community composition in digestive tracts of Litopenaeus vannamei and rearing water in biofloc aquaculture system

In this study, we investigated the bacterial diversity in rearing water, shrimp (Litopenaeus vannamei) stomach and intestine based on temperature and exposure to wheat flour (carbon source) to determine the correlation between microbial community and surrounding environment in the zero-water exchange shrimp biofloc technology (BFT) system. Three temperature levels of 29 °C (optimal temperature for shrimp growth), 25 °C (rearing water temperature in winter) and 34 °C (summer) were used. Wheat flour was added to groups L (at late stage) and E (at early stage), and sodium bicarbonate was added to group N (wheat flour not added) to adjust the pH. During the operation of the system, the water quality was retained in groups E and N, while it seriously deteriorated in group L at all temperatures. After wheat flour addition in group L, all water quality parameters were recovered efficiently. Using next generation sequencing (NGS) analysis, a total of 26 phyla and 340 OTUs at the genus level were identified in rearing water (the number of samples, n = 31), shrimp stomach (n = 57), and intestine (n = 57). Five phyla, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, and Bacteroidetes and 13 bacterial groups related to Phaeobacter, Pirellulaceae, Verrucomicrobiaceae, Rhodobacteraceae, Flavobacteriaceae, Amaricoccus, Marinicellaceae, Acidimicrobiales, C111, Planctomyces, Nitrosomonadaceae, koll13, and Piscirickettsiaceae were found in all samples, representing the core microbiome. Alpha diversity and richness were higher in the shrimp digestive tract, in group E, and at 25 °C compared with the others under each condition. Based on Unifrac PCoA analysis, the samples were clearly classified according to habitat and culture period mostly. The correlation analysis showed that carbon source addition (wheat flour) had a positive correlation with alkalinity and pH, while it was negatively correlated with total ammonia nitrogen (TAN), and nitrate-N concentration in the rearing water (P < 0.05). Temperature was not directly correlated with other environmental factors. The correlation between the core bacterial groups and various environmental factors were estimated. In the rearing water, most core bacterial groups except for major groups in Proteobacteria were negatively correlated with the concentration of nitrogen compounds and positively with alkalinity, pH, and wheat flour (P < 0.05), while the Proteobacteria groups showed opposite patterns. In the shrimp digestive tract, Planctomycetes and Actinobacteria groups positively correlated with culture period (growth stage or weight), while Proteobacteria and Verrucomicrobia groups were negatively correlated. In all habitats, most Actinobacteria were positively correlated with temperature, while Bacteroidetes were negatively correlated (P < 0.05). The present study demonstrated the correlation between environmental factors and major bacterial groups in the shrimp BFT system, and provided useful information to enhance the research and development of a new probiotic strategy and BFT management.

Incidence of microorganisms antagonistic to plant pathogenic fungi Bipolaris sorokiniana and Fusarium sp. in different soil communities

The antibiotic activity of conidia germination of the fungi Bipolaris sorokiniana and Fusarium sp. in the culture filtrate of the antagonistic microorganisms identified in different soil communities have been quantitatively assessed. According to the research results, among 54 tested soil bacteria isolates, 26 have manifested a verified antagonistic activity to Bipolaris sorokiniana, 27 – to Fusarium sp. (TIG6), 36 – to Fusarium sp. (Y7ec), 40 – to Fusarium sp. (T2ec), as proven by the results of the mathematical treatment of the collected data (statistical significance p<0.01). It should be noted that the greatest number of the antagonists to plant pathogenic fungi Bipolaris sorokiniana were found in the soil collected from underneath the wheat of the Tulunskaya-12 breed. The maximum number of the organisms antagonistic to fungi Fusarium sp. were found in the soil taken from underneath indoor plants and sod-meadow soil. Preliminary identification of the antagonistic soil bacteria has shown that the majority of the antagonistic bacteria represent the coryneform bacteria, including Arthrobacter sp. and Micobacterium sp., Bacillus sp. and Pseudomonas sp., Actinobacteria group. A cluster and factor analysis of the test cultures by their sensitivity to the culture filtrate of the soil bacteria showed that the greatest similarity in the reaction to the bacterial metabolites is demonstrated by the isolates of Fusarium sp. T2ec and Y7ec. Compared to all isolates of Fusarium sp., Bipolaris sorokiniana show a significantly different reaction to the metabolites produced by soil bacteria. The x2 criterion-based statistic analysis did not show any difference in the incidence of the antagonistic microorganisms in the used test cultures.

Phylogeny of the freshwater lineages within the phyla Actinobacteria (Overview)

This review presents molecular classification of freshwater Actinobacteria based on the phylogeny of the 16S rRNA gene. We show the classification of the entire phylum Actinobacteria and the taxonomic rank of freshwater lineages of Actinobacteria within this phylum. The discovery history of different groups of freshwater Actinobacteria is considered. We have systematized the information about the phylogeny of cultivated and uncultivated freshwater Actinobacteria and give their brief description. Data is provided on freshwater groups of Actinobacteria found in different ecotopes of Lake Baikal.

Divergent responses of taxonomic and predicted functional profiles of bacterioplankton to reservoir impoundment

Freshwater ecosystems are undergoing extensive human disturbance of dam construction which form large amounts of reservoirs and lead to dramatic changes in hydraulic conditions. Bacterioplankton are key component of aquatic ecosystems. Investigation on their taxonomic compositions and associated functions responded to reservoir operation is essential to understand the ecological consequence of dam construction. In this study, we use the Three Gorges Reservoir as a model system. High-throughput sequencing is used to investigate the bacterioplankton community composition, and the bioinformatic tool of Tax4Fun is applied to predict the potential metabolic functions responded to reservoir impoundment. Results show that the taxonomic communities of bacterioplankton are significantly impacted by impoundment. The dominant group of Actinobacteria which accounts for 17.0%–58.1% of the retrieved sequences significantly increases after impoundment on phylum level. The influences of impoundment appear to be more apparent on order level that the relative abundances of four groups including Frankiales, Sphingomonadales, Sphingobacteriales and SubsectionI of class Cyanobacteria significantly vary after impoundment. In contrast, the predicted functional communities of bacterioplankton remain relatively stable that most of predicted functional categories including methane and nitrogen metabolisms have no significant variation after impoundment. Besides, significant distance decay patterns appear on the taxonomic communities after impoundment rather than the predicted functional communities. The environmental variables show significant impacts on the taxonomic community rather than predicted functional community, whereas the spatial variables have no effect on both taxonomic and predicted functional communities. In general, the taxonomic and predicted functional communities of bacterioplankton exhibit divergent responses to the impoundment in reservoir.

Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments.

Energy-starved microbes in deep marine sediments subsist at near-zero growth for thousands of years, yet the mechanisms for their subsistence are unknown because no model strains have been cultivated from most of these groups. We investigated Baltic Sea sediments with single-cell genomics, metabolomics, metatranscriptomics, and enzyme assays to identify possible subsistence mechanisms employed by uncultured Atribacteria, Aminicenantes, Actinobacteria group OPB41, Aerophobetes, Chloroflexi, Deltaproteobacteria, Desulfatiglans, Bathyarchaeota, and Euryarchaeota marine group II lineages. Some functions appeared to be shared by multiple lineages, such as trehalose production and NAD+-consuming deacetylation, both of which have been shown to increase cellular life spans in other organisms by stabilizing proteins and nucleic acids, respectively. Other possible subsistence mechanisms differed between lineages, possibly providing them different physiological niches. Enzyme assays and transcripts suggested that Atribacteria and Actinobacteria group OPB41 catabolized sugars, whereas Aminicenantes and Atribacteria catabolized peptides. Metabolite and transcript data suggested that Atribacteria utilized allantoin, possibly as an energetic substrate or chemical protectant, and also possessed energy-efficient sodium pumps. Atribacteria single-cell amplified genomes (SAGs) recruited transcripts for full pathways for the production of all 20 canonical amino acids, and the gene for amino acid exporter YddG was one of their most highly transcribed genes, suggesting that they may benefit from metabolic interdependence with other cells. Subsistence of uncultured phyla in deep subsurface sediments may occur through shared strategies of using chemical protectants for biomolecular stabilization, but also by differentiating into physiological niches and metabolic interdependencies.IMPORTANCE Much of life on Earth exists in a very slow-growing state, with microbes from deeply buried marine sediments representing an extreme example. These environments are like natural laboratories that have run multi-thousand-year experiments that are impossible to perform in a laboratory. We borrowed some techniques that are commonly used in laboratory experiments and applied them to these natural samples to make hypotheses about how these microbes subsist for so long at low activity. We found that some methods for stabilizing proteins and nucleic acids might be used by many members of the community. We also found evidence for niche differentiation strategies, and possibly cross-feeding, suggesting that even though they are barely growing, complex ecological interactions continue to occur over ultralong timescales.

Screening and Molecular Characterization of Cellulase Producing Actinobacteria from Litchi Orchard

Background:Cellulolysis is of considerable economic importance in laundry detergents, textile and pulp and paper industries and in fermentation of biomass into biofuels.Objective:The aim was to screen cellulase producing actinobacteria from the fruit orchard because of its requirement in several chemical reactions.Methods:Strains of actinobacteria were isolated on Sabouraud’s agar medium. Similarities in cultural and biochemical characterization by growing the strains on ISP medium and dissimilarities among them perpetuated to recognise nine groups of actinobacteria. Cellulase activity was measured by the diameter of clear zone around colonies on CMC agar and the amount of reducing sugar liberated from carboxymethyl cellulose in the supernatant of the CMC broth. Further, 16S rRNA gene sequencing and molecular characterization were placed before NCBI for obtaining recognition with accession numbers.Results:Prominent clear zones on spraying Congo Red were found around the cultures of strains of three groups SK703, SK706, SK708 on CMC agar plates. The enzyme assay for carboxymethylcellulase displayed extra cellulase activity in broth: 0.14, 0.82 and 0.66 &amp;#181;mol mL-1 min-1, respectively at optimum conditions of 35°C, pH 7.3 and 96 h of incubation. However, the specific cellulase activities per 1 mg of protein did not differ that way. It was 1.55, 1.71 and 1.83 μmol mL-1 min-1. The growing mycelia possessed short compact chains of 10-20 conidia on aerial branches. These morphological and biochemical characteristics, followed by their verification by Bergey’s Manual, categorically allowed the strains to be placed under actinobacteria. Further, 16S rRNA gene sequencing, molecular characterization and their evolutionary relationship through phylogenetics also confirmed the putative cellulase producing isolates of SK706 and SK708 subgroups to be the strains of Streptomyces. These strains on getting NCBI recognition were christened as Streptomyces glaucescens strain SK91L (KF527284) and Streptomyces rochei strain SK78L (KF515951), respectively.Conclusion:Conclusive evidence on the basis of different parameters established the presence of cellulase producing actinobacteria in the litchi orchard which can convert cellulose into fermentable sugar.

Microbiomes of Top and Sub-Layers of Semi-Arid Soils in North-Eastern Nigeria Are Rich in Firmicutes and Proteobacteria with Surprisingly High Diversity of Rare Species

Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with drought, advancing desertification and degraded soils. Most restoration efforts involve revegetation, which in the past has met with limited success. Microbial communities of soils play a pivotal role in soil fertility and plant cover. We conducted the first metagenomic amplicon sequencing study, comparing two soil depths to determine whether soil bacteria abundance and diversity in the harsh bare soils were sufficient to sustain greening efforts. The goal was to glean insights to guide microbial inoculant formulation needed in the region. Samples from top (0 - 15 cm) and sub (16 - 65 cm) soils were collected from five strategic locations in the state. Using next generation Illumina sequencing protocols, total DNA extracted directly from the soils was sequenced and analyzed by QIIME. Metadata collected from site showed scorching temperatures of over 46˚C, near zero moisture level and a pH of about 6 for top soil. At 65 cm depth, the temperature averaged 32˚C with a pH of 5 and significantly higher soil moisture of 0.1%. The bacterial community structure was unexpectedly very diverse at both soil depths samples, recording a ChaO1 index ranging from 909 to 4296 and a Shannon diversity range of 3.54 to 6.33. The most abundant phyla in both soil depths were the Firmicutes and Proteobacteria; however the relative abundance of composite lower taxa was strikingly different. Operational taxonomic units and diversity indices were highest for top soils and were dominated by members of resilient groups of Actinobacteria, Firmucutes, Acidobacteria and numerous other less well-known taxa whose individual relative abundance did not exceed 3% of total population. The high diversity and richness of Proteobacteria (at 65 cm depth), some of which are key to soil fertility, suggest that revegetation efforts could be improved by shifting the gradient of these microbiota upwards using shades and micro-irrigation. Soils in semi-arid regions in Nigeria contain numerous operational taxonomic bacterial groups with potential thermophilic and drought genetic resources to be mined. Microbial community structure beneath the top soil appears stable and should be the target sample for the assessments of climatic change impact on microbial community structure in environments like this.

Pre-exposition to polycyclic aromatic hydrocarbons (PAHs) enhance biofilm formation and hydrocarbon removal by native multi-species consortium

In this work, a biofilm-mediated removal of polyaromatic hydrocarbons (PAHs) was proposed. PAHs are toxic and persistent contaminants from petroleum industry, dispersed on water, soils, air and sediments. The removal capabilities of C15 mixed culture of four indigenous strains of Pseudomonas and actinobacteria were successfully corroborated in a previous work. Results showed an interesting removal behavior of planktonic C15 consortium, with degradation capabilities notably enhanced when comparing with pure cultures. In the work reported in this paper, biofilm formation was evaluated in pure cultures and C15 defined consortium in order to propose a biofilm mediated immobilization strategy for bioremediation. Interestingly, a notable enhancement (approx. 180%) in biofilm formation was observed after mixing the four species of C15 compared with pure cultures. Phenanthrene and pyrene also stimulated biofilm arrangement and biofilm-immobilized microorganisms demonstrated a hydrocarbon removal significantly higher than planktonic cells. Maximal removal values were 100% for phenanthrene and 78% for pyrene, after 7 days incubation. The biodegradation assay was divided into two stages: biofilm formation and hydrocarbon removal. The importance of PAHs presence during biofilm formation was evaluated. Although no differences in biofilm structure were observed, bioemulsifier production was enhanced and removal was accelerated when phenanthrene and pyrene were added during biofilm formation stage. Even though more experiments must be conducted, considering the coexistence of Pseudomonas and actinobacteria groups during biodegradation and the improvement of removal performance, interspecies beneficial interactions could be suspected in this native multi-species biofilm.

A peptidome-based phylogeny pipeline reveals differential peptides at the strain level within Bifidobacterium animalis subsp. lactis

Bifidobacteria are gut commensal microorganisms belonging to the Actinobacteria group. Some specific strains of Bifidobacterium animalis subsp. lactis are used in functional foods as they are able to exert health-promoting effects in the human host. Due to the limited genetic variability within this subspecies, it is sometimes difficult for a manufacturer to properly track its strain once included in dairy products or functional foods. In this paper, we present a peptidome-based analysis in which the proteomes of a set of B. animalis subsp. lactis strains were digested in silico with human gut endopeptidases. The molecular masses were compared along all the strains to detect strain-specific peptides. These peptides may be interesting towards the development of methodologies for strain identification in the final product.

Bacteria as growth-promoting agents for citrus rootstocks

The microbial community plays an essential role in maintaining the ecological balance of soils. Interactions between microorganisms and plants have a major influence on the nutrition and health of the latter, and growth-promoting rhizobacteria can be used to improve plant development through a wide range of mechanisms. Therefore, the objective of the present study was to evaluate bacteria as growth-promoting agents for citrus rootstocks. A total of 30 bacterial isolates (11 of Bacillus spp., 11 actinobacteria, and 8 lactic acid bacteria) were evaluated in vitro for indoleacetic acid production, phosphate solubilization, and nitrogen (N) fixation. In vivo testing consisted of growth promotion trials of the bacterial isolates that yielded the best results on in vitro tests with three rootstocks: Swingle citrumelo [Citrus×paradisi Macfad cv. Duncan×Poncirus trifoliata (L.) Raf.], Sunki mandarin (Citrus sunki Hort. ex Tan), and rangpur (Citrus×limonia Osbeck). The parameters of interest were height, number of leaves, stem diameter, shoot and root dry mass, and total dry mass at 150days after germination. The results showed that most bacterial isolates were capable of IAA production. Only one lactic acid bacterium isolate (BL06) solubilized phosphate, with a high solubilization index (PSI>3). In the actinobacteria group, isolates ACT01 (PSI=2.09) and ACT07 (PSI=2.01) exhibited moderate phosphate-solubilizing properties. Of the Bacillus spp. isolates, only CPMO6 and BM17 solubilized phosphate. The bacterial isolates that most fixated nitrogen were BM17, ACT11, and BL24. In the present study, some bacteria were able to promote growth of citrus rootstocks; however, this response was dependent on plant genotype and isolate. Bacillus spp. BM16 and CPMO4 were able to promote growth of Swingle citrumelo. In Sunki mandarin plants, the best treatment results were obtained with BM17 (Bacillus sp.) and ACT11 (actinobacteria). For Rangpur lime rootstock, only BM05 (Bacillus sp.) was able to promote increase in two parameters assessed, height and number of leaves. When the bacterial isolates were used in mixture there was not promoted growth of plants on rootstocks. This fact may be associated with the different mechanisms of action of each bacteria involved or with the presence of competition among the microorganisms of the mixture.