Microbiology of barrier component analogues of a deep geological repository.

Canada is currently implementing a site selection process to identify a location for a deep geological repository (DGR) for the long-term storage of Canada's used nuclear fuel, wherein used nuclear fuel bundles will be sealed inside copper-coated carbon steel containers, encased in highly compacted bentonite clay buffer boxes, and sealed deep underground in a stable geosphere. Because a DGR must remain functional for a million years, it is important to examine ancient natural systems that serve as analogues for planned DGR components. Specifically, studying the microbiology of natural analogue components of a DGR is important for developing an understanding of the types of microorganisms that may be able to grow and influence the long-term stability of a DGR. This study explored the abundance, viability, and composition of microorganisms in several ancient natural analogues using a combination of cultivation and cultivation-independent approaches. Samples were obtained from the Tsukinuno bentonite deposit (Japan) that formed ∼10 mya, the Opalinus Clay formation (Switzerland) that formed ∼174 mya, and Canadian shield crystalline rock from Northern Ontario that formed ∼2.7 bya. Analysis of 16S rRNA gene amplicons revealed that three of the ten Tsukinuno bentonite samples analyzed were dominated by putative aerobic heterotrophs and fermenting bacteria from the phylum Actinobacteria, whereas five of the Tsukinuno bentonite samples were dominated by sequences associated with putative acidophilic chemolithoautotrophs capable of sulfur reduction. The remaining Tsukinuno bentonite samples, the Northern Ontario rock samples, and the Opalinus Clay samples generated inconsistent replicate 16S rRNA gene profiles and were associated primarily with contaminant sequences, suggesting that the microbial profiles detected were not sample-specific but spurious. Culturable aerobic heterotroph abundances were relatively low for all Tsukinuno bentonite samples, culturable anaerobic heterotrophs were only detected in half of the Tsukinuno samples, and sulfate-reducing bacteria (SRB) were only detected in one Tsukinuno sample by cultivation. Culture-specific 16S rRNA gene profiles from Tsukinuno clay samples demonstrated the presence of phyla Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes among aerobic heterotroph cultures and additional bacteria from the phyla Actinobacteria and Firmicutes from anaerobic heterotroph plate incubations. Only one nucleic acid sequence detected from a culture was also associated with its corresponding clay sample profile, suggesting that nucleic acids from culturable bacteria were relatively rare within the clay samples. Sequencing of DNA extracted from the SRB culture revealed that the taxon present in the culture was affiliated with the genus Desulfosporosinus, which has been found in related bentonite clay analyses. Although the crystalline rock and Opalinus Clay samples were associated with inconsistent, likely spurious 16S rRNA gene profiles, we show evidence for viable and detectable microorganisms within several Tsukinuno natural analogue bentonite samples.

Taxonomic classification of the bacterial endosymbiont Wolbachia based on next-generation sequencing: is there molecular evidence for its presence in tardigrades?

We used high-throughput sequencing of 16S rRNA to test whether tardigrade species are infected with Wolbachia parasites. We applied SILVA and Greengenes databases that allowed taxonomic classification of bacterial sequences to OTUs. The results obtained from both databases differed considerably in the number of OTUs, and only the Greengenes database allowed identification of Wolbachia (infection was also supported by comparison of sequences to NCBI database). The putative bacterial endosymbiont Wolbachia was discovered only in adult eutardigrades, while bacteria identified down to the order Rickettsiales were detected in both eutardigrade eggs and adult specimens. Nevertheless, the frequency of Wolbachia in the bacterial communities of the studied eutardigrades was low. Similarly, in our positive control, i.e., a fairy shrimp Streptocephalus cafer, which was found to be infected with Wolbachia in our previous study using Sanger sequencing, only the Rickettsiales were detected. We also carried out phylogenetic reconstruction using Wolbachia sequences from the SILVA and Greengenes databases, Alphaproteobacteria putative endosymbionts and Rickettsiales OTUs obtained in previous studies on the microbial community of tardigrades, and Rickettsiales and Wolbachia OTUs obtained in the current study. Our discovery of Wolbachia in tardigrades can fuel new research to uncover the specifics of this interaction.

Do methanotrophs drive phosphorus mineralization in soil ecosystem?

Experiments were carried out to elucidate linkage between methane consumption and mineralization of phosphorous (P) from different P sources. The treatments were (i) no CH4 + no P amendment (absolute control), (ii) with CH4 + no P amendment (control), (iii) with CH4 + inorganic P as Ca3(PO4)2, and (iv) with CH4 + organic P as sodium phytate. P sources were added at 25 µg P·(g soil)-1. Soils were incubated to undergo three repeated CH4 feeding cycles, referred to as feeding cycle I, feeding cycle II, and feeding cycle III. CH4 consumption rate k (µg CH4 consumed·(g soil)-1·day-1) was 0.297 ± 0.028 in no P amendment control, 0.457 ± 0.016 in Ca3(PO4)2, and 0.627 ± 0.013 in sodium phytate. Rate k was stimulated by 2 to 6 times over CH4 feeding cycles and followed the trend of sodium phytate > Ca3(PO4)2 > no P amendment control. CH4 consumption stimulated P solubilization from Ca3(PO4)2 by a factor of 2.86. Acid phosphatase (µg paranitrophenol released·(g soil)-1·h-1) was higher in sodium phytate than the no P amendment control. Abundance of 16S rRNA and pmoA genes increased with CH4 consumption rates. The results of the study suggested that CH4 consumption drives mineralization of unavailable inorganic and organic P sources in the soil ecosystem.

Endophytic bacterial communities and spatiotemporal variations in cotton roots in Xinjiang, China.

Endogenous bacteria are important for maintaining the health and other ecologically relevant functions of cotton plants. However, little is known about the community structures and diversity of endophytic bacteria in cotton plants. In our study, we used the Illumina amplicon sequencing technology to study the endophytic bacteria found in cotton root tissue in Xinjiang, China. A total of 60.84 × 106 effective sequences of the 16S rRNA gene in the V5-V6 variable region revealed a large number of operational taxonomic units (OTUs), namely 81-338 OTUs, at a cut-off level of 3% and a sequencing depth of 50 000 sequences. Among the 23 classes identified, Gammaproteobacteria was the dominant group, followed by Alphaproteobacteria, Actinobacteria, and Bacillus. The diversity of endogenous bacteria differed at different growth periods, with the most OTUs detected in seedlings (654), followed by the budding stage (381), flowering stage (350), and flocking stage (351). A total of 217 OTUs were common to all four stages. Pantoea tags were more common to the Shihezi region, whereas Erwinia labels were more common to the Hami region. These results suggest that the dynamics of endophytic bacterial communities are affected by plant growth stage. This highlights the relevance of microbial diversity studies in improving our understanding of endophyte communities.

Diversity and space-time dynamics of the bacterial communities in cotton (Gossypium hirsutum) rhizosphere soil.

Rhizosphere bacteria are key determinants of plant health and productivity. In this study, we used PCR-based next-generation sequencing to reveal the diversity and community composition of bacteria in the cotton rhizosphere from samples collected in Xinjiang Province, China. We identified 125 bacterial classes within 49 phyla from these samples. Proteobacteria (33.07% of total sequences), Acidobacteria (19.88%), and Gemmatimonadetes (11.19%) dominated the bacterial community. Marked differences were evident in the α-diversity of rhizosphere bacteria during different cotton plant growth and development stages. The operational taxonomic unit (OTU) numbers were highest in seedling and bud stages and decreased at the flowering and fruit-boll-opening stages. Forty-three OTUs from the Proteobacteria were common to all four periods of cotton development. Proteobacteria were more abundant in the rhizospheres of cotton from southern Xinjiang than from northern Xinjiang, while the opposite trend was observed for Acidobacteria. Gemmatimonadetes frequency was broadly the same in both northern and southern Xinjiang. These results suggest that there is abundant diversity in the microbiota of cotton rhizosphere soil. Proteobacteria and Actinobacteria dominated this microbial niche and bacterial communities in the seedling, bud, flowering, and boll-opening stages appear to be more similar to one another than to communities at the other growth stages.

Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada.

Rhizosphere and root associated bacteria are key components of plant microbiomes and influence crop production. In sustainable agriculture, it is important to investigate bacteria diversity in various plant species and how edaphic factors influence the bacterial microbiome. In this study, we used high-throughput sequencing to assess bacterial communities associated with the rhizosphere and root interior of canola, wheat, field pea, and lentil grown at four locations in Saskatchewan, Canada. Rhizosphere bacteria communities exhibited distinct profiles among crops and sampling locations. However, each crop was associated with distinct root endophytic bacterial communities, suggesting that crop species may influence the selection of root bacterial microbiome. Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla in the root interior, whereas Gemmatimonadetes, Firmicutes, and Acidobacteria were prevalent in the rhizosphere soil. Pseudomonas and Stenotrophomonas were predominant in the rhizosphere and root interior, whereas Acinetobacter, Arthrobacter, Rhizobium, Streptomyces, Variovorax, and Xanthomonas were dominant in the root interior of all crops. The relative abundance of specific bacterial groups in the rhizosphere correlated with soil pH and silt and organic matter contents; however, there was no correlation between root endophytes and analyzed soil properties. These results suggest that the root microbiome may be modulated by plant factors rather than soil characteristics.

Co-occurrence patterns among prokaryotes across an age gradient in pit mud of Chinese strong-flavor liquor.

It is widely believed that the quality and characteristics of Chinese strong-flavor liquor (CSFL) are closely related to the age of the pit mud; CSFL produced from older pit mud tastes better. This study aimed to investigate the alteration and interaction of prokaryotic communities across an age gradient in pit mud. Prokaryotic microbes in different-aged pit mud (1, 6, and 10 years old) were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. Analysis of the 16S rRNA gene indicated that the prokaryotic community was significantly altered with pit mud age. There was a significant increase in the genera Methanosarcina, Methanobacterium, and Aminobacterium with increased age of pit mud, while the genus Lactobacillus showed a significant decreasing trend. Network analysis demonstrated that both synergetic co-occurrence and niche competition were dominated by 68 prokaryotic genera. These genera formed 10 hubs of co-occurrence patterns, mainly under the phyla Firmicutes, Euryarchaeota, and Bacteroidetes, playing important roles on ecosystem stability of the pit mud. Environmental variables (pH, NH4+, available P, available K, and Ca2+) correlated significantly with prokaryotic community assembly. The interaction of prokaryotic communities in the pit mud ecosystem and the relationship among prokaryotic communities and environmental factors contribute to the higher quality of the pit mud in older fermentation pits.

Variety features differentiate microbiota in the grape leaves.

The dependence of plant health and crop quality on the epiphytic microbial community has been extensively addressed, but little is known about plant-associated microbial communities under natural conditions. In this study, the bacterial and fungal communities on grape leaves were analyzed by 16S rRNA gene and internal transcribed spacer high-throughput sequencing, respectively. The results showed differences in the composition of the microbial communities on leaf samples of nine wine grape varieties. The most abundant bacterial genus was Pseudomonas, and the top three varieties with Pseudomonas were Zinfandel (22.6%), Syrah (21.6%), and Merlot (13.5%). The most abundant fungal genus was Alternaria, and the cultivar with the lowest abundance of Alternaria was Zinfandel (33.6%), indicating that these communities had different habitat preferences. The linear discriminant analysis effect size of all species showed that the bacteria Enterococcus, Massilia, and Kocuria were significantly enriched on the leaves of Merlot, Syrah, Cabernet Sauvignon, respectively; Pseudomonadales and Pantoea on Zinfandel; and Bacillus, Turicibacter, and Romboutsia on Pinot Noir. Similarly, the fungi Cladosporium, Phoma, and Sporormiella were significantly enriched on Zinfandel, Lon, and Gem, respectively. Both Bray-Curtis and unweighted UniFrac revealed that bacteria and fungi have a significant impact (P < 0.01), and the results further proved that variety is the most important factor affecting the microbial community. The findings indicate that some beneficial or harmful microorganisms existing on the wine grape leaves might affect the health of the grape plants and the wine-making process.

Effect of bamboo vinegar powder as an antibiotic alternative on the digesta bacteria communities of finishing pigs.

This study investigated the use for bamboo vinegar powder as an antibiotic alternative in the diet of growing-finishing pigs by examining their digestive bacterial communities. Forty-five Duroc × Landrace × Yorkshire growing-finishing pigs were randomly allocated to five diet groups: 0%, 0.5%, 1.0%, or 1.5% bamboo vinegar levels and antibiotics. After 37 days, the digesta in duodenum of four pigs from each treatment were analyzed for their bacterial community compositions using 16S rRNA gene sequencing. The addition of 1.5% bamboo vinegar powder had an effect on the intestinal microflora most similar to that of antibiotics, indicating its potential to promote the growth and development of finishing pigs. We also found the 1.5% bamboo vinegar powder group to have an increased abundance of Firmicutes/Bacteroidetes compared with the other bamboo vinegar powder groups, which may enhance the ability of the host to absorb food energy and store more body fat. Additionally, the effects of bamboo vinegar powder on promoting the abundances of Lactobacillus and Thalassospira and on inhibiting Streptococcus and Prevotella growth revealed it may play an important role in animal production. Moreover, functional predictions of microbes via PICRUSt indicated that feed supplemented with 1.5% bamboo vinegar powder could promote many vital metabolic pathways.

Microbial diversity and community structure in agricultural soils suffering from 4 years of Pb contamination.

Heavy metal pollution has become a widespread environmental problem due to rapid economic development. The phylogenetic diversity and structure of microbial communities in lead (Pb)-contaminated Lou soils were investigated using Illumina MiSeq sequencing of 16S rRNA genes. The presence of Pb2+ in soil showed weak impact on the diversity of soil bacteria community, but it influenced the abundance of some genera of bacteria, as well as soil physicochemical properties. We found significant differences in the relative abundances of heavy-metal-resistant bacteria such as Bacillus, Streptococcus, and Arthrobacter at the genus level. Available Pb and total Pb negatively correlated with soil organic matter but positively affected available phosphorus. The abundance of main bacteria phyla was highly correlated with total Pb. The relative abundance of Gemmatimonadetes, Nitrospirae, and Planctomycetes was negatively correlated with total Pb. Collectively, Pb influences both the microbial community composition and physicochemical properties of soil.

Effects of exogenous microbial inoculum on the structure and dynamics of bacterial communities in swine carcass composting.

Composting is a widely accepted method for the disposal of deceased livestock. It is a biological self-heating process during which animal carcasses are converted to fertilizer products. Additional inoculants can facilitate the composting progress. This study investigated how the addition of microbial inoculants could improve the composting effectiveness and could change the structure and dynamics of bacterial communities in the carcass composting process. Four strains of Bacillus were inoculated into the swine carcass composting piles. The groups with the additional inoculants showed a higher temperature in the thermophilic phase and higher germination indices in the composted products. The sequencing results showed that the dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria, and the dominant classified genera were Brevibacterium and Bacillus. Canonical correlation analysis showed that temperature and moisture exerted a stronger influence on the bacterial community diversity. The interaction network of dominant genera and the abundance variation of the bacterial community demonstrated that the inoculated bacterial agent changed the structure of bacterial communities and enriched the diversity of the species due to antagonism and symbiosis among the dominant bacterial communities.

Seasonal dynamics of the bacterioplankton community in a large, shallow, highly dynamic freshwater lake.

The spatiotemporal shifts of the bacterioplankton community can mirror their transition of functional traits in an aquatic ecosystem. However, the spatiotemporal variation of the bacterioplankton community composition structure (BCCS) within a large, shallow, highly dynamic freshwater lake is still poorly understood. Here, we examined the seasonal and spatial variability of the BCCs within Poyang Lake by sequencing the 16S rRNA gene amplicon to explore how hydrological changes affect the BCCs. Principal coordinate analysis showed that the BCCs varied significantly among four sampling seasons, but not spatially. The seasonal changes of the BCCs were mainly attributed to the differences between autumn and spring-winter. Higher α diversity indices were observed in autumn. Redundancy analysis indicated that the BCCs co-variated with water level, pH, temperature, total phosphorus, ammoniacal nitrogen, electrical conductivity, total nitrogen, and turbidity. Among them, water level was the key determinant separating autumn BCCs from the BCCs in other seasons. A significantly lower relative abundance of Burkholderiales (betI and betVII) and a higher relative abundance of Actinomycetales (acI, acTH1, and acTH2) were found in autumn than in other seasons. Overall, our results suggest that water level changes associated with pH, temperature, and nutrient status shaped the seasonal patterns of the BCCs within Poyang Lake.

Lower dietary concentrate level increases bacterial diversity in the rumen of Cervus elaphus yarkandensis.

The ruminal microbiota plays major roles in feed digestion. The composition and fermentation of the bacterial communities in 3 important ruminant species have been studied previously. Here, we extended this research to the effect of concentrate-to-forage ratios on ruminal bacterial communities in Tarim red deer (Cervus elaphus yarkandensis). Different concentrate-to-forage ratios (2:8, 3:7, 4:6, and 5:5) were fed to Tarim red deer for 20 days. Ruminal bacterial communities were elucidated by 16S ribosomal RNA gene sequencing on an Illumina HiSeq 2500 platform. The microbial composition and biodiversity at the different concentrate-to-forage ratio levels were analyzed using clustering of operational taxonomic units based on 97% sequence identity, taxonomic classification at the phylum and genus levels, α diversity, and ß diversity. Rumen microorganisms of deer fed a diet with a concentrate-to-forage ratio of 2:8 had the highest species diversity, followed by ratios of 3:7, 4:6, and 5:5. The community structure of the A1 and A2 samples and the A3 and A4 samples was similar. The bacterial composition appeared to be affected by diet, with a lower dietary concentrate level tending to increase the richness and diversity of ruminal bacteria in the rumen of Tarim red deer.

Phylloplane bacteria of Jatropha curcas: diversity, metabolic characteristics, and growth-promoting attributes towards vigor of maize seedling.

The complex role of phylloplane microorganisms is less understood than that of rhizospheric microorganisms in lieu of their pivotal role in plant's sustainability. This experiment aims to study the diversity of the culturable phylloplane bacteria of Jatropha curcas and evaluate their growth-promoting activities towards maize seedling vigor. Heterotrophic bacteria were isolated from the phylloplane of J. curcas and their 16S rRNA genes were sequenced. Sequences of the 16S rRNA gene were very similar to those of species belonging to the classes Bacillales (50%), Gammaproteobacteria (21.8%), Betaproteobacteria (15.6%), and Alphaproteobacteria (12.5%). The phylloplane bacteria preferred to utilize alcohol rather than monosaccharides and polysaccharides as a carbon source. Isolates exhibited ACC (1-aminocyclopropane-1-carboxylic acid) deaminase, phosphatase, potassium solubilization, and indole acetic acid (IAA) production activities. The phosphate-solubilizing capacity (mg of PO4 solubilized by 108 cells) varied from 0.04 to 0.21. The IAA production potential (µg IAA produced by 108 cells in 48 h) of the isolates varied from 0.41 to 9.29. Inoculation of the isolates to maize seed significantly increased shoot and root lengths of maize seedlings. A linear regression model of the plant-growth-promoting activities significantly correlated (p < 0.01) with the growth parameters. Similarly, a correspondence analysis categorized ACC deaminase and IAA production as the major factors contributing 41% and 13.8% variation, respectively, to the growth of maize seedlings.

Effects of several in-feed antibiotic combinations on the abundance and diversity of fecal microbes in weaned pigs.

To characterize the effects of several subtherapeutic antibiotic combinations on the abundance and diversity of fecal microbes, 400 weaned pigs were selected and randomly assigned to 8 groups, where they were continuously fed different antibiotic combinations for 28 days. Then, a total of 48 pigs were randomly selected to collect feces samples for DNA extraction and 16S rRNA high-throughput sequencing. Compared with that of pigs without antibiotic administration, the diversities of fecal microbes were decreased in the pigs fed chlortetracycline (CTC), olaquindox (OLA), and either enramycin (ER) or virginiamycin (VIR), and the relative abundances of members of the phylum Bacteroidetes and the genus Prevotella were increased. Compared with that of pigs without antibiotic administration, the relative abundances of members of the phylum Proteobacteria and the genus Succinivibrio were decreased in the pigs fed CTC, a mixture of zinc bacitracin (ZB) + colistin sulfate (COL), a mixture of CTC+ZB+COL, a mixture of CTC+OLA, or a mixture of CTC+OLA+ER. α-Diversity and ß-diversity were decreased (P < 0.05) in the pigs fed ZB+COL or a mixture of CTC+OLA+ER or CTC+OLA+VIR. This study provides experimental data to deepen our understanding on the effects of antibiotic combinations on intestinal microbes.

From source to filter: changes in bacterial community composition during potable water treatment.

Rural communities rely on surface water reservoirs for potable water. Effective removal of chemical contaminants and bacterial pathogens from these reservoirs requires an understanding of the bacterial community diversity that is present. In this study, we carried out a 16S rRNA-based profiling approach to describe the bacterial consortia in the raw surface water entering the water treatment plants of 2 rural communities. Our results show that source water is dominated by the Proteobacteria, Bacteroidetes, and Cyanobacteria, with some evidence of seasonal effects altering the predominant groups at each location. A subsequent community analysis of transects of a biological carbon filter in the water treatment plant revealed a significant increase in the proportion of Proteobacteria, Acidobacteria, Planctomycetes, and Nitrospirae relative to raw water. Also, very few enteric coliforms were identified in either the source water or within the filter, although Mycobacterium was of high abundance and was found throughout the filter along with Aeromonas, Legionella, and Pseudomonas. This study provides valuable insight into bacterial community composition within drinking water treatment facilities, and the importance of implementing appropriate disinfection practices to ensure safe potable water for rural communities.

Seasonal variation in an acid mine drainage microbial community.

Environmental oxidation and microbial metabolism drive production of acid mine drainage (AMD). Understanding changes in the microbial community, due to geochemical and seasonal characteristics, is fundamental to AMD monitoring and remediation. Using direct sequencing of the 16S and 18S rRNA genes to identify bacterial, archaeal, and eukaryotic members of the microbial community at an AMD site in Northern Ontario, Canada, we found a dynamic community varying significantly across winter and summer sampling times. Community composition was correlated with physical and chemical properties, including water temperature, pH, conductivity, winter ice thickness, and metal concentrations. Within Bacteria, Acidithiobacillus was the dominant genus during winter (11%-57% of sequences) but Acidiphilium was dominant during summer (47%-87%). Within Eukarya, Chrysophyceae (1.5%-94%) and Microbotrymycetes (8%-92%) dominated the winter community, and LKM11 (4%-62%) and Chrysophyceae (25%-87%) the summer. There was less diversity and variability within the Archaea, with similar summer and winter communities mainly comprising Thermoplasmata (33%-64%) and Thermoprotei (5%-20%) classes but also including a large portion of unclassified reads (∼40%). Overall, the active AMD community varied significantly between winter and summer, with changing community profiles closely correlated to specific differences in AMD geochemical and physical properties, including pH, water temperature, ice thickness, and sulfate and metal concentrations.

Archaeal ammonia oxidizers respond to soil factors at smaller spatial scales than the overall archaeal community does in a high Arctic polar oasis.

Archaea are ubiquitous and highly abundant in Arctic soils. Because of their oligotrophic nature, archaea play an important role in biogeochemical processes in nutrient-limited Arctic soils. With the existing knowledge of high archaeal abundance and functional potential in Arctic soils, this study employed terminal restriction fragment length polymorphism (t-RFLP) profiling and geostatistical analysis to explore spatial dependency and edaphic determinants of the overall archaeal (ARC) and ammonia-oxidizing archaeal (AOA) communities in a high Arctic polar oasis soil. ARC communities were spatially dependent at the 2-5 m scale (P < 0.05), whereas AOA communities were dependent at the ∼1 m scale (P < 0.0001). Soil moisture, pH, and total carbon content were key edaphic factors driving both the ARC and AOA community structure. However, AOA evenness had simultaneous correlations with dissolved organic nitrogen and mineral nitrogen, indicating a possible niche differentiation for AOA in which dry mineral and wet organic soil microsites support different AOA genotypes. Richness, evenness, and diversity indices of both ARC and AOA communities showed high spatial dependency along the landscape and resembled scaling of edaphic factors. The spatial link between archaeal community structure and soil resources found in this study has implications for predictive understanding of archaea-driven processes in polar oases.

Isolation of plant-growth-promoting rhizobacteria from rhizospheric soil of halophytes and their impact on maize (Zea mays L.) under induced soil salinity.

The present investigation was aimed to scrutinize the salt tolerance potential of plant-growth-promoting rhizobacteria (PGPR) isolated from rhizospheric soil of selected halophytes (Atriplex leucoclada, Haloxylon salicornicum, Lespedeza bicolor, Suaeda fruticosa, and Salicornica virginica) collected from high-saline fields (electrical conductivity 4.3-5.5) of District Mardan, Pakistan. Five PGPR strains were identified using 16S rRNA amplification and sequence analysis. Bacillus sp., isolated from rhizospheric soil of Atriplex leucoclada, and Arthrobacter pascens, isolated from rhizospheric soil of Suaeda fruticosa, are active phosphate solubilizers and bacteriocin and siderophore producers; hence, their inoculation and co-inoculation on maize ('Rakaposhi') under induced salinity stress enhanced shoot and root length and shoot and root fresh and dry mass. The accumulation of osmolytes, including sugar and proline, and the elevation of antioxidant enzymes activity, including superoxide dismutase, peroxidase, catalase, and ascorbate peroxidase, were enhanced in the maize variety when inoculated and co-inoculated with Bacillus sp. and Arthrobacter pascens. The PGPR (Bacillus sp. and A. pascens) isolated from the rhizosphere of the mentioned halophytes species showed reliability in growth promotion of maize crop in all the physiological parameters; hence, they can be used as bio-inoculants for the plants growing under salt stress.

Investigation and analysis of microbiological communities in natural Ophiocordyceps sinensis.

Ophiocordyceps sinensis is a fungus that parasitizes caterpillars, and more than 30 species of filamentous fungi have been isolated from its fruiting body. However, its microbiological diversity remains unclear. Based on the clone library and quantitative PCR techniques, the bacterial flora and mycobiota of 3 different samples (larva, stromata/sclerotia, and surface soil) from natural O. sinensis specimens were investigated using primer sets that targeted the 16S rRNA gene and internal transcribed spacer region of ribosomal DNA. The results showed that the abundance of bacterial and fungal communities in the soil attached to the surface of O. sinensis was (6.4 ± 1.4) × 10(6) and (6.0 ± 0.3) × 10(7) copies/g dry matter, respectively, which was the highest compared with that in the larva and stromal samples. The main groups of bacteria in the O. sinensis samples were Proteobacteria and Actinobacteria, while Ascomycota was the most dominant fungal group in the 3 samples. At the genus level, Geomyces, Phoma, and Trichocladium were the dominant genera in the larval sample, while Geomyces and Cladosporium were the dominant genera in the stromal sample. In conclusion, a great number of bacterial and fungal species were present in naturally occurring O. sinensis specimens, and there was a high diversity of bacterial and fungal communities. These findings contribute to the understanding of the bacterial and fungal community structure of this valuable medicinal fungus and lay the foundation for the future discovery of new medicinal microorganism resources.