Biodiversity of a Burkholderia cepacia population isolated from the maize rhizosphere at different plant growth stages

Food grade plastics and Bisphenol A: Associated risks, toxicity, and bioremediation approaches

Bisphenols' widespread use in day to day life has enabled its existence in various compartments of the environment. Bisphenol A (BPA) is utilized as a monomer in manufacturing polycarbonate plastics, epoxy resins, as well as flame retardants and is also considered as an endocrine disruptor. This study focuses on determining BPA concentration in daily-use food-grade plastic containers, in addition to its toxicity evaluation in environmental samples contaminated by BPA leachates. The highest concentration of BPA was observed in black poly bags (42.78 ppm), followed by slice juice bottles and infant milk bottles. Toxicity tests revealed significant impacts on Rhizobium and Chlorella sp. as a representative species of soil and aquatic environment respectively. To biodegrade the BPA, two potential strains, Brucella sp. and Brevibacillus parabrevis, were isolated from a landfill site. Qualitative and quantitative evaluation of biodegraded BPA through U-HPLC and GC-MSMS showed various metabolites of BPA. Results indicate the native bacterial isolates as potential candidates for BPA degradation while transforming this contaminant to a less toxic and hazardous form. The study also proposes the risk associated with food-grade plastic containers and recommends to establish a sustainable way for plastic waste management.

Microdiversity sustains the distribution of rhizosphere-associated bacterial species from the root surface to the bulk soil region in maize crop fields

Over the years, the microbial community of maize (Zea mays) rhizosphere has been extensively studied; however, the role of microdiversity sustain rhizosphere-associated microbial species distribution from root surface to bulk soil in mature maize is still unclear. Although operational taxonomic units (OTUs) have been used to classify species, amplicon sequence variants (ASVs) have been shown to be effective in representing microdiversity within OTUs at a finer genetic scale. Therefore, the aim of this study was to examine the role of microdiversity in influencing the distribution of rhizosphere-associated microbial species across environmental gradients from root surface to bulk soil at the OTU and ASV levels. Here, the microbial community structures of bulk, loosely bound, and tightly bound soil samples from maize rhizosphere were examined at OTU and ASV levels. The results showed that OTU and ASV methods exhibited similar microbial community structures in rhizosphere. Additionally, different ecotypes with varying distributions and habitat preferences were observed within the same bacterial OTU at the ASV level, indicating a rich bacterial microdiversity. In contrast, the fungal community exhibited low microdiversity, with no significant relationship between fungal microdiversity and persistence and variability. Moreover, the ecotypes observed within the bacterial OTUs were found to be positively or negatively associated with environmental factors, such as soil organic carbon (SOC), NO3 --N, NH4 +-N contents, and pH. Overall, the results showed that the rich microdiversity could sustain the distribution of rhizosphere-associated bacterial species across environmental gradients from root surface to bulk soil. Further genetic analyses of rhizosphere-associated bacterial species could have considerable implications for potential mediation of microdiversity for sustainable crop production.

Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels

Soil aggregates contain distinct physio-chemical properties across different size classes. These differences in micro-habitats support varied microbial communities and modulate the effect of plant on microbiome, which affect soil functions such as disease suppression. However, little is known about how the residents of different soil aggregate size classes are impacted by plants throughout their growth stages. Here, we examined how tomato plants impact soil aggregation and bacterial communities within different soil aggregate size classes. Moreover, we investigated whether aggregate size impacts the distribution of soil pathogen and their potential inhibitors. We collected samples from different tomato growth stages: before-planting, seedling, flowering, and fruiting stage. We measured bacterial density, community composition, and pathogen abundance using qPCR and 16 S rRNA gene sequencing. We found the development of tomato growth stages negatively impacted root-adhering soil aggregation, with a gradual decrease of large macro-aggregates (1-2 mm) and an increase of micro-aggregates (<0.25 mm). Additionally, changes in bacterial density and community composition varied across soil aggregate size classes. Furthermore, the pathogen exhibited a preference to micro-aggregates, while macro-aggregates hold a higher abundance of potential pathogen-inhibiting taxa and predicted antibiotic-associated genes. Our results indicate that the impacts of tomatoes on soil differ for different soil aggregate size classes throughout different plant growth stages, and plant pathogens and their potential inhibitors have different habitats within soil aggregate size classes. These findings highlight the importance of fine-scale heterogeneity of soil aggregate size classes in research on microbial ecology and agricultural sustainability, further research focuses on soil aggregates level could help identify candidate tax involved in suppressing pathogens in the virtual micro-habitats.

Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America

As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.

Growth performance of Listeria monocytogenes and background microbiota from mushroom processing environments

Interaction between Listeria monocytogenes and resident background microbiota may occur in food processing environments and may influence the survival of this pathogen in a factory environment. Therefore the aim of this study was to characterize the growth performance of microbiota isolated from the processing environments of frozen sliced mushrooms, and to investigate the competitive performance of L. monocytogenes when co-cultured with accompanying environmental microbiota. Acinetobacter, Enterobacteriaceae, Lactococcus and Pseudomonas were the most prominent background microbiota isolated from the processing environment of frozen sliced mushrooms. All individual microbiota strains were able to grow and form biofilm in filter-sterilized mushroom medium, with the mannitol-consumers Raoultella and Ewingella as top performers, reaching up to 9.6 and 9.8 log CFU/mL after 48 h incubation at room temperature. When L. monocytogenes mushroom isolates were co-cultured with the microbiota strains, L. monocytogenes counts ranged from 7.6 to 8.9 log CFU/mL after 24 h of incubation, while counts of the microbiota strains ranged from 5.5 to 9.0 log CFU/mL. Prolonged incubation up to 48 h resulted in further increase of L. monocytogenes counts when co-cultured with non-acidifying species Pseudomonas and Acinetobacter reaching 9.1 to 9.2 log CFU/mL, while a decrease of L. monocytogenes counts reaching 5.8 to 7.7 log CFU/mL was observed in co-culture with Enterobacteriaceae and acidifying Lactococcus representatives. In addition, L. monocytogenes grew also in spent mushroom media of the microbiota strains, except in acidified spent media of Lactococcus strains. These results highlight the competitive ability of L. monocytogenes during co-incubation with microbiota in fresh and in spent mushroom medium, indicative of its invasion and persistence capacity in food processing factory environments.

Ready-To-Eat Rocket Salads as Potential Reservoir of Bacteria for the Human Microbiome

Reportedly, Western-type diets may induce the loss of key microbial taxa within the gastrointestinal microbiota, promoting the onset of noncommunicable diseases. It was hypothesized that the consumption of raw vegetables could contribute to the maintenance of the intestinal microbial community structure. In this context, we explored bacteria associated with commercial rocket salads produced through different farming practices: traditional (conventional, organic, and integrated) and vertical farming. Viable counts of mesophilic bacteria and lactic acid bacteria (LAB) were performed on plate count agar (PCA) and de Man-Rogosa-Sharpe (MRS) agar at pH 5.7, whereas metataxonomics through 16S rRNA gene sequencing was used to profile total bacteria associated with rocket salads. We found that rocket salads from vertical farming had much fewer viable bacteria and had a bacterial community structure markedly different from that of rocket salads from traditional farming. Furthermore, although α- and β-diversity analyses did not differentiate rocket samples according to farming techniques, several bacterial taxa distinguished organic and integrated from conventional farming salads, suggesting that farming practices could affect the taxonomic composition of rocket bacterial communities. LAB were isolated from only traditional farming samples and belonged to different species, which were variably distributed among samples and could be partly associated with farming practices. Finally, the INFOGEST protocol for in vitro simulation of gastrointestinal digestion revealed that several taxonomically different rocket-associated bacteria (particularly LAB) could survive gastrointestinal transit. This study suggests that commercial ready-to-eat rocket salads harbor live bacteria that possess the ability to survive gastrointestinal transit, potentially contributing to the taxonomic structure of the human gut microbiota. IMPORTANCE Western-type diets are composed of foods with a reduced amount of naturally occurring microorganisms. It was hypothesized that a microbe-depleted diet can favor the alteration of the human intestinal microbial ecosystem, therefore contributing to the onset of chronic metabolic and immune diseases currently recognized as the most significant causes of death in the developed world. Here, we studied the microorganisms that are associated with commercial ready-to-eat rocket salads produced through different farming practices. We showed that rocket salad (a widely consumed vegetal food frequently eaten raw) may be a source of lactic acid bacteria and other microbes that can survive gastrointestinal transit, potentially increasing the biodiversity of the intestinal microbiota. This deduction may be valid for virtually all vegetal foods that are consumed raw.

Biodegradation of malathion by Micrococcus sp. strain MAGK3: kinetics and degradation fragments

Malathion is widely used as an agricultural insecticide, but its toxic nature makes it a serious environmental contaminant. To screen indigenous bacteria for malathion degradation, a strain MAGK3 capable of utilizing malathion as its sole carbon and energy source was isolated from Pennisetum glaucum agricultural soil. Based on morphological and biochemical characteristics and 16S rDNA sequence analysis, strain MAGK3 was identified as Micrococcus aloeverae. The strain was cultured in the presence of malathion under aerobic and energy-restricting conditions, and it grew well in MSM containing malathion (1000 µl/L), showing the highest specific growth rate at 500 µl/L_. Reverse-phase UHPLC-DAD analysis indicated that 100%, 90.48%, 84.27%, 75.46%, 66.65%, and 31.96% of malathion were degraded within 15 days in liquid culture augmented with 50, 100, 200, 300, 500, and 1000 µl/L concentrations of commercial malathion, respectively. Confirmation of malathion degradation to malathion mono, diacids, and phosphorus moiety was performed by Q-TOF-MS analysis, and a pathway of biodegradation was proposed. The influence of co-substrates was also examined to optimize biodegradation further. Kinetic studies based on different models were conducted, and the results demonstrated good conformity with the first-order model. Malathion degradation process by Micrococcus aloeverae was characterized by R² of 0.95, and the initial concentration was reduced by 50% i.e. (DT50) in 8.11 d at an initial concentration of 500 µl/L. This establishes the Micrococcus sp. as a potent candidate for active bioremediation of malathion in liquid cultures as it can withstand high malathion load and can possibly impact the development strategies of bioremediation for its elimination.

Validation and Evaluation of Plant Growth Promoting Potential of Rhizobacteria Towards Paddy Plants

This study aimed to characterize, validate, and evaluate the plant growth potential of bacterial isolates (E-2, T-2, and T-1) to determine their suitability for application as biofertilizers and/or plant-biostimulants. The plant growth-promoting potential of bacteria (E-2, T-2, and T-1) has been validated in a hydroponic study on paddy plants by inoculating bacterial isolates and monitoring the phenotypic and plant growth responses. The applicability of bacteria was tested based on their tolerance to salinity, susceptibility to antibiotics, and identification based on 16S rDNA sequencing. The isolates E-2, T-2, and T-1 improved plant growth variably and significantly (P < 0.05 at 95% confidence interval) when inoculated into the plant growth matrix, ensuring nutrient availability to the plants grown under a nutrient (nitrate or phosphate) deprived growth matrix. Isolates E-2, T-2, and T-1 grew at salt (NaCl) concentrations of 7%, 6%, and 6%, respectively, and were tolerant to saline conditions. Although these three isolates exhibited resistance to certain antibiotics, they were susceptible to a large number of readily available antibiotics. Isolates E-2, T-2, and T-1 were identified as Klebsiella sp. strain BAB-6433, Citrobacter freundii strain R2A5, and Citrobacter sp. DY1981 respectively, and all of these may be assigned to Risk-Group-2 and hence are safe in view of their susceptibility to readily available antibiotics. Hence, these isolates are promising for extensive evaluation as bioinoculants to ecologically improve soil quality, fertility, crop growth, and yield.

The Response to Inoculation with PGPR Plus Orange Peel Amendment on Soybean Is Cultivar and Environment Dependent

Plant growth-promoting rhizobacteria (PGPR) effects on plant yield are highly variable under field conditions due to competition with soil microbiota. Previous research determined that many Bacillus velezensis PGPR strains can use pectin as a sole carbon source and that seed inoculation with PGPR plus pectin-rich orange peel (OP) can enhance PGPR-mediated increases in plant growth. Because the previous studies used a single soybean cultivar, the objective of this research was to test the effect of PGPR plus OP inoculation on plant responses in a wide range of soybean cultivars. Preliminary screening with 20 soybean cultivars in the greenhouse showed that the PGPR plus OP produced a positive increase in all plant growth parameters when all cultivar data was averaged. However, when the inoculation response was examined cultivar by cultivar there was a range of cultivar response from a 60% increase in growth parameters to a 12% decrease, pointing to the presence of a cultivar-PGPR specificity. Further greenhouse and field experiments that studied cultivars with contrast responses to synbiotic inoculation revealed that the environment and/or the molecular interactions between the plant and microorganisms may play an important role in plant responsiveness.

Non-Rhizobial Endophytes Associated with Nodules of Vigna radiata L. and Their Combined Activity with Rhizobium sp

Root nodules of legume plants are devoted for hosting endophytic symbiotic bacteria that fix atmospheric nitrogen but recently proved as a niche for various non-rhizobial endophytes (NRE) also. In the present investigation, one rhizobial and two NRE were isolated and characterized as Rhizobium sp. AAU B3, Bacillus sp. AAU B6 and Bacillus sp. AAU B12. These isolates were studied for in vitro biocontrol activity against two pathogenic fungi. NRE isolates exhibited antifungal activity against root rot causing Macrophomina phaseolina (ITCC-6749) isolated from Vigna radiata and wilt causing pathogen Fusarium udum Butler isolated from Cajanus cajan in liquid as well as on solid medium. Furthermore, their antagonism was increased markedly when combined with Rhizobium sp. Moreover, Bacillus sp. AAU B6 showed amplification of the zwittermicin A gene (~ 950 bp) which is evident for the production of antibiotics. All three isolates showed HCN production in vitro also, Bacillus sp. AAU B12 exhibited amplification of its gene hcnC. Pathogenic fungal hyphae became thin, transparent, and bent as well as fungi lost their normal growth and branching patterns when exposed to volatile compounds produced by NRE. All the 3 isolates produced siderophores, however siderophore production was increased considerably when all three strains are mixed together. Furthermore, all the three isolates produced cell wall degrading enzymes (chitinase, protease, and cellulase) but lipolytic activity was exhibited only by Rhizobium sp. AAU B3. When NRE inoculated in combination of Rhizobium; overcomes the disease severity against M. phaseolina under pot study. Thus, from present study it is concluded that co-inoculation of NRE and Rhizobium sp. can be exploited as biocontrol bio-agents against M. phaseolina in green gram at field levels.

Comparative analysis of different methods used for molecular characterization of Burkholderia cepacia complex isolated from noncystic fibrosis conditions

PURPOSE

Burkholderia is a Gram-negative opportunistic bacterium capable of causing severe nosocomial infections. The aim of this study was to characterize Burkholderia cepacia complex and to compare different molecular methods used in its characterization.

METHODS

In this study, 45 isolates of Burkholderia cepacia complex (Bcc) isolated from clinical cases were subjected to RAPD (Random amplified polymorphic DNA), recA-RFLP (Restriction fragment length polymorphism), 16SrDNA-RFLP, whole-cell protein analysis, recA DNA sequencing and biofilm assay.

RESULTS

Of the 45 isolates tested, 97.7% were sensitive to ceftazidime, 82.2% were sensitive to Cotrimoxazole, 73.3% were sensitive to meropenem, 55.5% were sensitive to minocycline and 42.2% were sensitive to levofloxacin. Majority of the isolates harbored all the tested virulence genes except bpeA and cblA. The RAPD generated 11 groups (R1-R11), recA-RFLP 10 groups (A1-A10), 16SrRNA-RFLP 5 groups (S1-S5) and SDS-PAGE (Sodium Dodecyl Sulphate-Polyacrylamide gel electrophoresis) whole cell protein analysis revealed 12 groups (C1-C12). recA sequencing revealed that most of the isolates belonging to the genomovar III Burkholderia cenocepacia. Though all the methods are found to be efficient in differentiating Burkholderia spp., recA-RFLP was highly discriminatory at 96% similarity value. The study also identified a new strain Burkholderia pseudomultivorans for the first time in the country. Further, recA sequencing could identify the strains to species level. Majority of the multidrug-resistant strains also showed moderate to strong biofilm-forming ability, which further contributes to the virulence characteristics of the pathogens.

CONCLUSIONS

The study highlights the importance of combination of molecular methods to characterize Burkholderia cepacia complex. Molecular typing of these human pathogens yields important information for the clinicians in order to initiate the most appropriate therapy in the case of severe infections and to implement preventive measures for the effective control of transmission of Burkholderia spp.

Tillage, Mulching and Nitrogen Fertilization Differentially Affects Soil Microbial Biomass, Microbial Populations and Bacterial Diversity in a Maize Cropping System

Determination of biologically active components of the soil organic matter, such as soil microbial biomass carbon (C) and nitrogen (N) can be used as indicators for variations in soil productivity due to changes in soil management. Soil agronomic management practices bring about changes in the physical and chemical properties of the soil, resulting in variations in soil microbial biomass and microbial diversity. The effects of tillage, mulch and inorganic fertilizers on soil microbial biomass C and N, microbial populations and bacterial diversity were determined from the treatment combinations which had been applied for 5 years in Central Kenyan Highlands. The test crop used was maize (Zea mays L.). The study involved conventional and minimum tillage systems, mulching and inorganic fertilizers (120 kg N/ha). Tillage (P &lt; 0.001), mulch (P &lt; 0.001), and fertilizer (P = 0.009) significantly affected soil microbial biomass C and N whereby minimum tillage and mulch increased soil microbial biomass C and N. Interestingly, minimum tillage and mulch recorded the highest bacteria and fungi CFUs compared to conventional tillage and inorganic fertilizers. Only fertilizer and mulch (P &lt; 0.001) had significant effect on actinobacteria CFUs. Amplified ribosomal DNA analysis (ARDRA) showed that the highest genetic distance of 0.611 was recorded between treatments conventional tillage + no mulch + no NPK fertilizer and conventional tillage + no mulch + NPK fertilizer. The results demonstrate that minimum tillage and mulching are attractive soil agronomic management practices since they increase soil microbial biomass and bacterial diversity in agricultural soils.

Disease-Suppressive Soils-Beyond Food Production: a Critical Review

In the pursuit of higher food production and economic growth and increasing population, we have often jeopardized natural resources such as soil, water, vegetation, and biodiversity at an alarming rate. In this process, wider adoption of intensive farming practices, namely changes in land use, imbalanced fertilizer application, minimum addition of organic residue/manure, and non-adoption of site-specific conservation measures, has led to declining in soil health and land degradation in an irreversible manner. In addition, increasing use of pesticides, coupled with soil and water pollution, has led the researchers to search for an environmental-friendly and cost-effective alternatives to controlling soil-borne diseases that are difficult to control, and which significantly limit agricultural productivity. Since the 1960s, disease-suppressive soils (DSS) have been identified and studied around the world. Soil disease suppression is the reduction in the incidence of soil-borne diseases even in the presence of a host plant and inoculum in the soil. The disease-suppressive capacity is mainly attributed to diverse microbial communities present in the soil that could act against soil-borne pathogens in multifaceted ways. The beneficial microorganisms employ some specific functions such as antibiosis, parasitism, competition for resources, and predation. However, there has been increasing evidence on the role of soil abiotic factors that largely influence the disease suppression. The intricate interactions of the soil, plant, and environmental components in a disease triangle make this process complex yet crucial to study to reduce disease incidence. Increasing resistance of the pathogen to presently available chemicals has led to the shift from culturable microbes to unexplored and unculturable microbes. Agricultural management practices such as tillage, fertilization, manures, irrigation, and amendment applications significantly alter the soil physicochemical environment and influence the growth and behaviour of antagonistic microbes. Plant factors such as age, type of crop, and root behaviour of the plant could stimulate or limit the diversity and structure of soil microorganisms in the rhizosphere. Further, identification and in-depth of disease-suppressive soils could lead to the discovery of more beneficial microorganisms with novel anti-microbial and plant promoting traits. To date, several microbial species have been isolated and proposed as key contributors in disease suppression, but the complexities as well as the mechanisms of the microbial and abiotic interactions remain elusive for most of the disease-suppressive soils. Thus, this review critically explores disease-suppressive attributes in soils, mechanisms involved, and biotic and abiotic factors affecting DSS and also briefly reviewing soil microbiome for anti-microbial drugs, in fact, a consequence of DSS phenomenon.

Soil Microbiome Manipulation Gives New Insights in Plant Disease-Suppressive Soils from the Perspective of a Circular Economy: A Critical Review

This review pays attention to the newest insights on the soil microbiome in plant disease-suppressive soil (DSS) for sustainable plant health management from the perspective of a circular economy that provides beneficial microbiota by recycling agro-wastes into the soil. In order to increase suppression of soil-borne plant pathogens, the main goal of this paper is to critically discuss and compare the potential use of reshaped soil microbiomes by assembling different agricultural practices such as crop selection; land use and conservative agriculture; crop rotation, diversification, intercropping and cover cropping; compost and chitosan application; and soil pre-fumigation combined with organic amendments and bio-organic fertilizers. This review is seen mostly as a comprehensive understanding of the main findings regarding DSS, starting from the oldest concepts to the newest challenges, based on the assumption that sustainability for soil quality and plant health is increasingly viable and supported by microbiome-assisted strategies based on the next-generation sequencing (NGS) methods that characterize in depth the soil bacterial and fungal communities. This approach, together with the virtuous reuse of agro-wastes to produce in situ green composts and organic bio-fertilizers, is the best way to design new sustainable cropping systems in a circular economy system. The current knowledge on soil-borne pathogens and soil microbiota is summarized. How microbiota determine soil suppression and what NGS strategies are available to understand soil microbiomes in DSS are presented. Disturbance of soil microbiota based on combined agricultural practices is deeply considered. Sustainable soil microbiome management by recycling in situ agro-wastes is presented. Afterwards, how the resulting new insights can drive the progress in sustainable microbiome-based disease management is discussed.

The survival rate and efficiency of non-encapsulated and encapsulated native starter cultures to improve the quality of artisanal game meat sausages

This study addresses the application of native, multiple strain starter cultures for standardization of game meat sausages production. The designed starter cultures consisting of two indigenous Lactobacillus sakei and one Leuconostoc mesenteroides strains. These strains were used in both, the encapsulated and non-encapsulated form, in the game meat dough, individually or in combination, with eight treatments in total. Microbiological and physicochemical characteristics of the sausages were monitored throughout the manufacturing process, while sensory properties, biogenic amine content, and volatile compounds were evaluated in the final products. As revealed by rep-PCR, native starter cultures, encapsulated or non-encapsulated, had survived the whole sausage production process; however, to varying degrees. The application of indigenous decarboxylase negative Lb. sakei strains significantly (P < 0.05) reduced tyramine content, rapidly decreased pH and promoted the number reduction of Enterobacteriaceae and elimination of E. coli, L. monocytogenes and coliforms in ready-to-eat products. A total of 84 volatile compounds were identified by SPME-GC-MS in the eight treatment batches of game meat sausages, with only minor differences between the treatments. No significant differences in sensory traits (P > 0.05) between tested treatments were found, although treatment with the Lb. sakei strains received the highest scores for the sensory traits including cross-section, odour, hardness, aroma, and overall acceptability. Combination of multi-strain Lb. sakei starter cultures resulted in growth prevention of undesirable microbiota, reduction of tyramine content and increased the acceptability parameters of full-ripened sausages, which make them good candidates for industrial as well as artisanal application.

Priming maize seeds with cyanobacteria enhances seed vigour and plant growth in elite maize inbreds

Biofilm formation of a nitrogen-fixing cyanobacterium Anabaena torulosa with a beneficial fungus Trichoderma viride (An-Tr) was examined under laboratory conditions. A gradual enhancement in growth over A. torulosa alone was recorded in the biofilm, with 15-20% higher values in nitrogen fixation, IAA and exopolysaccharide production illustrating the synergism among the partners in the biofilm. To investigate the role of such biofilms in priming seed attributes, mesocosm studies using primed seeds of two maize inbred lines (V6, V7) were undertaken. Beneficial effects of biofilm (An-Tr) were recorded, as compared to uninoculated treatment and cyanobacterial consortium (Anabaena-Nostoc; BF 1-4) at both stages (7 and 21 DAS, days after sowing) with a significant increase of more than 20% in seedling attributes, along with 5-15% increment in seed enzyme activities. More than three- to fivefold higher values in nitrogen fixation and C-N mobilizing enzyme activities, and significant increases in leaf chlorophyll, proteins and PEP carboxylase activity were observed with V7-An-Tr biofilm. Cyanobacterial inoculation brought about distinct changes in the soil phospholipid fatty acid profiles (PLFA); particularly, significant changes in those representing eukaryotes and anaerobic bacteria. Principal component analyses illustrated the significant role of dehydrogenase activity and microbial biomass carbon and distinct elicited effects on soil microbial communities, as evidenced by the PLFA. This investigation highlighted the promise of cyanobacteria as valuable priming options to improve mobilization of nutrients at seed stage, modulating the abundance and activities of various soil microbial communities, thereby, enhanced plant growth and vigour of maize plants.

Lactic Acid Bacteria Isolation from Spontaneous Sourdough and Their Characterization Including Antimicrobial and Antifungal Properties Evaluation

This research effort aimed at isolating and phenotypically characterizing lactic acid bacteria (LAB) isolates from a spontaneous rye sourdough manufactured following traditional protocols, as well as at evaluating their antimicrobial and antifungal properties as key features for future industrial applications. Thirteen LAB strains of potential industrial interest were isolated and identified to species-level via PCR. Most of the sourdough isolates showed versatile carbohydrate metabolisms. The Leuconostoc mesenteroides No. 242 and Lactobacillus brevis No. 173 demonstrated to be gas producers; thus, revealing their heterofermenter or facultative homofermenter features. Viable counts higher than 7.0 log10 (CFU/mL) were observed for Lactobacillus paracasei No. 244, Lactobacillus casei No. 210, L. brevis No. 173, Lactobacillus farraginis No. 206, Pediococcus pentosaceus No. 183, Lactobacillus uvarum No. 245 and Lactobacillus plantarum No. 135 strains, after exposure at pH 2.5 for 2 h. Moreover, L. plantarum No. 122, L. casei No. 210, Lactobacillus curvatus No. 51, L. paracasei No. 244, and L. coryniformins No. 71 showed growth inhibition properties against all the tested fifteen pathogenic strains. Finally, all LAB isolates showed antifungal activities against Aspergillus nidulans, Penicillium funiculosum, and Fusarium poae. These results unveiled the exceptionality of spontaneous sourdough as a source of LAB with effective potential to be considered in the design of novel commercial microbial single/mixed starter cultures, intended for application in a wide range of agri-food industries, where the antimicrobial and antifungal properties are often sought and necessary. In addition, metabolites therefrom may also be considered as important functional and bioactive compounds with high potential to be employed in food and feed, as well as cosmetic and pharmaceutical applications.

The Influence of Meat Batter Composition and Sausage Diameter on Microbiota and Sensory Traits of Artisanal Wild Boar Meat Sausages

In this study, the influence of meat batter composition and sausage diameter on the development of microbiota and sensory traits of traditional, spontaneously fermented wild boar meat sausages are evaluated. This research also demonstrates how principal component analysis (PCA) can be used to relate product sensory properties to particular microbial genotype and to select potential starter or adjunct culture. Generally, similar microbiological results were obtained in all types of products. The undesirable microbiota was either not detected at any sausage production stage or its number decreased below the detection limit in ripened sausages. The low growth rate of lactic acid bacteria (LAB) was consistent with the obtained pH and slow acidification rate. Although no differences in the composition of LAB species were noticed between sausage types (50S=50% wild boar meat in small casing, 50L=50% wild boar meat in large casing, 100S=100% wild boar meat in small casing), a clear separation based on LAB genotypes could be observed. Upon quantitative descriptive analysis, significant differences in sensory attributes between sausage types were established. According to the PCA, the overall acceptability traits of sausages are closely linked to one Leuconostoc mesenteroides genotype (LM_4). Of all tested technological properties, LM_4 strains showed remarkable acidification ability, lowering the pH from pH=5.41 to 3.74, and pronounced proteolytic activity on skimmed milk as well as antagonistic activity against Staphylococcus aureus (DSM 20231) and Brochothrix thermosphacta (LMG 17208). Lipolytic and haemolytic activities were not detected, and all analyzed strains were susceptible to tested antibiotics and possessed no biogenic amine genes.

The Impact of Soil-Applied Biochars From Different Vegetal Feedstocks on Durum Wheat Plant Performance and Rhizospheric Bacterial Microbiota in Low Metal-Contaminated Soil

Biochar shapes the soil environment and plant growth. Nevertheless, the mechanisms associated with an improved plant biomass and soil microbiome in low metal-contaminated soils are still unclear. In this study, the influence of biochar on soil physico-chemical properties, plant performance, and rhizosphere microbiota in durum wheat was investigated at the above- and belowground levels. Two kinds of biochar from different feedstocks (wood chips and wheat straw pellets) and two Italian durum wheat varieties, Duilio and Marco Aurelio, were analyzed in a greenhouse using a low-nutrient gleyic fluvisol containing a very small amount of Pb and Zn. Four different treatments were performed: soil-only control (C), soil amended with woody biochar equilibrated with nutrient solution (B1+) and non-activated (B1−), and soil amended with non-activated (B2−) wheat straw biochar. Seven weeks after seed germination, (1) the physico-chemical properties of soil, biochars, and mixtures were assessed; (2) the fresh and dry weight of aboveground plant tissues and roots and other morphometric traits were measured; and (3) metabarcoding of the 16S rRNA bacterial gene was performed on rhizosphere soil samples. The results showed that the biochar from wheat straw had stronger impact on both durum varieties, with higher electrical conductivity, higher levels of available K and Na, and a substantial increase of dissolved Na+, K+, and Cl− ions in pore water. Generally, biochar amendment decreased Zn availability for the plants. In addition, biochar improved plant growth in the early growth stage, and the more positive effect was achieved by combining wheat straw biochar with Marco Aurelio. Rhizosphere bacterial microbiota showed variation in alpha diversity only due to treatment; on the other hand, the differential analysis showed consistent variation among samples with significant effects on amplicon sequence variant (ASV) abundance due to the specific biochar treatment as well as the genotype. The pure B1−, due to its scarce nutrient content with respect to the richer types (B1+ and B2−), had a negative impact on microbiota richness. Our study highlights that an appropriate combination of biochar feedstock and crop species may lead to superior yield.

Bacterial rhizosphere community profile at different growth stages of Umorok (Capsicum chinense) and its response to the root exudates

The role of microflora is an indispensable part of the living organisms. Plants actively recruit specific microbial community to establish favorable habitat with the distinct microbiome, essentially unique for each species, offering new opportunities for plant growth and productivity. Umorok, an indigenous chili variety of northeastern India, production is highly affected by various factors; therefore, rhizosphere bacteria and their relationship with the root exudates released were analyzed to demonstrate rhizosphere bacterial impact on plant growth and health. Culturable and metagenomic bacterial DNA was characterized and the chemical nature of the root exudate was analyzed using chemotaxis assay after its basic analysis in HPLC. Juvenile stage exhibited diverse bacterial species of gammaproteobacteria, alphaproteobacteria, and actinobacteria but lacked the betaproteobacteria while the microbial diversity was reduced in flowering and fruiting stages. However, every growth stage maintained a similar amount of bacterial population regardless of diversity. The population of Pseudomonas, Bacillus, and Burkholderia species was increased several folds in flowering and fruiting stage. Further, the chemotaxis assay unveiled the advantage of root exudate chemical composition for specific microbial recruitment. The chemical composition analysis of root exudates showed substantial variation in the concentration of organic acids, phenolics, and flavonoids that are favoring unique bacterial species. Thus, root exudates confer and limit the related microbial population besides typical plant-bacterial synergetic association. This study emphasized information about the type of microbial load present in each growth stage, which is essential to develop a microbial consortia package for Umorok overall crop improvement.

The Impact of Soil-Applied Biochars From Different Vegetal Feedstocks on Durum Wheat Plant Performance and Rhizospheric Bacterial Microbiota in Low Metal-Contaminated Soil

Biochar shapes the soil environment and plant growth. Nevertheless, the mechanisms associated with an improved plant biomass and soil microbiome in low metal-contaminated soils are still unclear. In this study, the influence of biochar on soil physico-chemical properties, plant performance, and rhizosphere microbiota in durum wheat was investigated at the above- and belowground levels. Two kinds of biochar from different feedstocks (wood chips and wheat straw pellets) and two Italian durum wheat varieties, Duilio and Marco Aurelio, were analyzed in a greenhouse using a low-nutrient gleyic fluvisol containing a very small amount of Pb and Zn. Four different treatments were performed: soil-only control (C), soil amended with woody biochar equilibrated with nutrient solution (B1+) and non-activated (B1-), and soil amended with non-activated (B2-) wheat straw biochar. Seven weeks after seed germination, (1) the physico-chemical properties of soil, biochars, and mixtures were assessed; (2) the fresh and dry weight of aboveground plant tissues and roots and other morphometric traits were measured; and (3) metabarcoding of the 16S rRNA bacterial gene was performed on rhizosphere soil samples. The results showed that the biochar from wheat straw had stronger impact on both durum varieties, with higher electrical conductivity, higher levels of available K and Na, and a substantial increase of dissolved Na+, K+, and Cl- ions in pore water. Generally, biochar amendment decreased Zn availability for the plants. In addition, biochar improved plant growth in the early growth stage, and the more positive effect was achieved by combining wheat straw biochar with Marco Aurelio. Rhizosphere bacterial microbiota showed variation in alpha diversity only due to treatment; on the other hand, the differential analysis showed consistent variation among samples with significant effects on amplicon sequence variant (ASV) abundance due to the specific biochar treatment as well as the genotype. The pure B1-, due to its scarce nutrient content with respect to the richer types (B1+ and B2-), had a negative impact on microbiota richness. Our study highlights that an appropriate combination of biochar feedstock and crop species may lead to superior yield.

The Draft Genome Sequence of Burkholderia sp. Strain Nafp2/4-1b Confirms Its Ability To Produce the Plant Growth-Promoting Traits Pyoverdine Siderophores, 1-Aminocyclopropane-1-Carboxylate Deaminase, and the Phytohormone Auxin

Burkholderia sp. strain Nafp2/4-1b is a rhizobacterium isolated from the rhizosphere of grassland in South Africa. This draft genome report confirms the presence of genes related to iron acquisition, alleviation of abiotic stress in plants, and other essential traits of plant growth-promoting rhizobacteria (PGPR) that signify the potential of this strain as a plant growth-promoting agent.

Metagenomic study of bacterial microbiota in persistent endodontic infections using Next-generation sequencing

AIM

To determine the bacterial microbiota in root canals associated with persistent apical periodontitis and their relationship with the clinical characteristics of patients using next-generation sequencing (NGS).

METHODOLOGY

Bacterial samples from root canals associated with teeth having persistent apical periodontitis were taken from 24 patients undergoing root canal retreatment. Bacterial DNA was extracted, and V3-V4 variable regions of the 16S rRNA gene were amplified. The amplification was deep sequenced by Illumina technology to establish the metagenetic relationships among the bacterial species identified. The composition and diversity of microbial communities in the root canal and their relationships with clinical features were analysed. Parametric and nonparametric tests were used to analyse differences between patient characteristics and microbial data.

RESULTS

A total of 86 different operational taxonomic units (OTUs) were identified and Good's nonparametric coverage estimator method indicated that 99.9 ± 0.00001% diversity was recovered per sample. The largest number of bacteria belonged to the phylum Proteobacteria. According to the medical history from the American Society of Anesthesiologists (ASA) Classification System, ASA II-III had higher richness estimates and distinct phylogenetic relationships compared to ASA I individuals (P < 0.05). Periapical index (PAI) score 5 was associated with increased microbiota diversity in comparison to PAI score 4, and this index was reduced in symptomatic patients.

CONCLUSIONS

Based on the findings of this study, it is possible to suggest a close relationship between several clinical features and greater microbiota diversity with persistent endodontic infections. This work provides a better understanding on how microbial communities interact with their host and vice versa.

Subfunctionalization influences the expansion of bacterial multidrug antibiotic resistance

Background

Antibiotic resistance is a major problem for human health. Multidrug resistance efflux pumps, especially those of the Resistance-Nodulation-Cell Division (RND) family, are major contributors to high-level antibiotic resistance in Gram-negative bacteria. Most bacterial genomes contain several copies of the different classes of multidrug resistance efflux pumps. Gene duplication and gain of function by the duplicate copies of multidrug resistance efflux pump genes plays a key role in the expansion and diversification of drug-resistance mechanisms.

Results

We used two members of the Burkholderia RND superfamily as models to understand how duplication events affect the antibiotic resistance of these strains. First, we analyzed the conservation and distribution of these two RND systems and their regulators across the Burkholderia genus. Through genetic manipulations, we identified both the exact substrate range of these transporters and their eventual interchangeability. We also performed a directed evolution experiment, combined with next generation sequencing, to evaluate the role of antibiotics in the activation of the expression of these systems. Together, our results indicate that the first step to diversify the functions of these pumps arises from changes in their regulation (subfunctionalization) instead of functional mutations. Further, these pumps could rewire their regulation to respond to antibiotics, thus maintaining high genomic plasticity.

Conclusions

Studying the regulatory network that controls the expression of the RND pumps will help understand and eventually control the development and expansion of drug resistance.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4222-4) contains supplementary material, which is available to authorized users.

Phenotypic and genotypic characterization of phosphate solubilizing bacteria and their efficiency on the growth of maize

Phosphate solubilizing bacteria (PSB) has ability to convert insoluble form of phosphorous to an available form. Applications of PSB as inoculants increase the phosphorus uptake by plant in the agriculture field. In this study, isolation and identification of PSB were carried out in Indian agriculture field (Nainital region, Uttarakhand). A total of 8 phosphate solubilizing bacterial colonies were isolated on the Pikovskaya’s (PKV) agar medium, containing insoluble tricalcium phosphate (TCP). The colonies showed clear halo zones around the bacterial growth were considered as phosphate solubilizers. Out of 8 bacterial isolates, 3 isolates showed high phosphate solubilization index (PSI) ranged from 4.88 ± 0.69 to 4.48 ± 0.30, lower pH ranging 3.08 ± 0.08 to 3.82 ± 0.12 and high phosphate solubilization varied from 305.49 ± 10 μg/ml to 277.72 ± 1.45 μg/ml, were selected for further characterization. Based on the 16 S rRNA gene sequence analysis A4 isolate and H6 isolate were closely related to Alcaligenes aquatilis (99%), and C1 isolate was closely related to Burkholderia cepacia (99%). In addition, pot examination also showed the greatest efficiency in promotion of maize growth compared to uninoculated plant. Isolated PSB were able to produce different organic acids (such as gluconic acids, formic acid, and citric acid) in the culture supernatant and may consider as the principle mechanism for phosphate solubilization. This study clearly indicates that A4, C1 and H6 isolates may use as a biofertilizers in ecological agricultural systems instead of synthetic chemicals and may help to sustain environmental health and soil productivity.

Elucidating and Regulating the Acetoin Production Role of Microbial Functional Groups in Multispecies Acetic Acid Fermentation

Acetoin (3-hydroxy-2-butanone) formation in vinegar microbiota is crucial for the flavor quality of Zhenjiang aromatic vinegar, a traditional vinegar produced from cereals. However, the specific microorganisms responsible for acetoin formation in this centuries-long repeated batch fermentation have not yet been clearly identified. Here, the microbial distribution discrepancy in the diacetyl/acetoin metabolic pathway of vinegar microbiota was revealed at the species level by a combination of metagenomic sequencing and clone library analysis. The results showed that Acetobacter pasteurianus and 4 Lactobacillus species (Lactobacillus buchneri, Lactobacillus reuteri, Lactobacillus fermentum, and Lactobacillus brevis) might be functional producers of acetoin from 2-acetolactate in vinegar microbiota. Furthermore, A. pasteurianus G3-2, L. brevis 4-22, L. fermentum M10-3, and L. buchneri F2-5 were isolated from vinegar microbiota by a culture-dependent method. The acetoin concentrations in two cocultures (L. brevis 4-22 plus A. pasteurianus G3-2 and L. fermentum M10-3 plus A. pasteurianus G3-2) were obviously higher than those in monocultures of lactic acid bacteria (LAB), while L. buchneri F2-5 did not produce more acetoin when coinoculated with A. pasteurianus G3-2. Last, the acetoin-producing function of vinegar microbiota was regulated in situ via augmentation with functional species in vinegar Pei After 72 h of fermentation, augmentation with A. pasteurianus G3-2 plus L. brevis 4-22, L. fermentum M10-3, or L. buchneri F2-5 significantly increased the acetoin content in vinegar Pei compared with the control group. This study provides a perspective on elucidating and manipulating different metabolic roles of microbes during flavor formation in vinegar microbiota.

IMPORTANCE

Acetoin (3-hydroxy-2-butanone) formation in vinegar microbiota is crucial for the flavor quality of Zhenjiang aromatic vinegar, a traditional vinegar produced from cereals. Thus, it is of interest to understand which microbes are driving the formation of acetoin to elucidate the microbial distribution discrepancy in the acetoin metabolic pathway and to regulate the metabolic function of functional microbial groups in vinegar microbiota. Our study provides a perspective on elucidating and manipulating different metabolic roles of microbes during flavor formation in vinegar microbiota.

Crop management as a driving force of plant growth promoting rhizobacteria physiology

Crop management systems influence plant productivity and nutrient use efficiency, as well as plant growth-promoting rhizobacteria (PGPR), which are known to influence the growth of plants via phytohormone production, phosphate solubilization, nitrogen (N) fixation and antimicrobial activity. The objective of this study was to compare the influence of two crop management system on microbial PGPR features. PGPR isolated from the rhizospheres of Carica papaya L. grown under two distinct management systems (conventional and organic) were identified and characterized. The 12 strains most efficient in solubilizing inorganic phosphate belonged to the genera Burkholderia, Klebsiella, and Leclercia. N fixation was observed in the strains B. vietnamiensis from the conventional farming system and B. vietnamiensis, B. cepacia and Leclercia sp. from the organic farming system. The B. vietnamiensis, B. cepacia, Klebsiella sp. and Klebsiella sp. isolates showed antifungal activity, while Leclercia sp. did not. The strains B. vietnamiensis and Enterobcter sp. (isolated from the conventional farming system) and Klebsiella sp. (isolated from the organic farming system) were efficient at solubilizing phosphate, producing phytohormones and siderophores, and inhibiting the mycelial growth of various phytopathogenic fungi (Botrytis cinerea, Pestalotia sp., Alternaria sp., Phoma sp., Fusarium culmorum, Geotrichum candidum). Physiological differences between the isolates from the two crop management regimes were distinguishable after 10 years of distinct management.

Biodegradation of Ochratoxin A by Bacterial Strains Isolated from Vineyard Soils

Ochratoxin A (OTA) is a mycotoxin with a main nephrotoxic activity contaminating several foodstuffs. In the present report, five soil samples collected from OTA-contaminated vineyards were screened to isolate microorganisms able to biodegrade OTA. When cultivated in OTA-supplemented medium, OTA was converted in OTα by 225 bacterial isolates. To reveal clonal relationships between isolates, molecular typing by using an automated rep-PCR system was carried out, thus showing the presence of 27 different strains (rep-PCR profiles). The 16S-rRNA gene sequence analysis of an isolate representative of each rep-PCR profiles indicated that they belonged to five bacterial genera, namely Pseudomonas, Leclercia, Pantoea, Enterobacter, and Acinetobacter. However, further evaluation of OTA-degrading activity by the 27 strains revealed that only Acinetobacter calcoaceticus strain 396.1 and Acinetobacter sp. strain neg1, consistently conserved the above property; their further characterization showed that they were able to convert 82% and 91% OTA into OTα in six days at 24 °C, respectively. The presence of OTα, as the unique OTA-degradation product was confirmed by LC-HRMS. This is the first report on OTA biodegradation by bacterial strains isolated from agricultural soils and carried out under aerobic conditions and moderate temperatures. These microorganisms might be used to detoxify OTA-contaminated feed and could be a new source of gene(s) for the development of a novel enzymatic detoxification system.

Does nature make provision for backups in the modification of bacterial community structures?

Self-balancing is an inherent character in nature in response to community structure modification pressure and modern biotechnology has revolutionized the way such detections are made. Presented here is an overview of the forces and process interactions between released bacteria and indigenous microflora which encompass soil bacterial diversity, community structure, indigenous endorhizosphere micro-organisms, molecular detection methodologies, and transgenic plants and microbes. Issues of soil bacterial diversity and community structure as well as the interpretation of results from various findings are highlighted and discussed as inferred from research articles. An understanding of the factors influencing bio-inoculant modification of bacterial community structure in the colonization of the rhizosphere is essential for improved establishment of biocontrol agents, and is critically reviewed.

Exserohilum rostratum: characterization of a cross-kingdom pathogen of plants and humans

Pathogen host shifts represent a major source of new infectious diseases. There are several examples of cross-genus host jumps that have caused catastrophic epidemics in animal and plant species worldwide. Cross-kingdom jumps are rare, and are often associated with nosocomial infections. Here we provide an example of human-mediated cross-kingdom jumping of Exserohilum rostratum isolated from a patient who had received a corticosteroid injection and died of fungal meningitis in a Florida hospital in 2012. The clinical isolate of E. rostratum was compared with two plant pathogenic isolates of E. rostratum and an isolate of the closely related genus Bipolaris in terms of morphology, phylogeny, and pathogenicity on one C3 grass, Gulf annual rye grass (Lolium multiflorum), and two C4 grasses, Japanese stilt grass (Microstegium vimineum) and bahia grass (Paspalum notatum). Colony growth and color, as well as conidia shape and size were the same for the clinical and plant isolates of E. rostratum, while these characteristics differed slightly for the Bipolaris sp. isolate. The plant pathogenic and clinical isolates of E. rostratum were indistinguishable based on morphology and ITS and 28S rDNA sequence analysis. The clinical isolate was as pathogenic to all grass species tested as the plant pathogenic strains that were originally isolated from plant hosts. The clinical isolate induced more severe symptoms on stilt grass than on rye grass, while this was the reverse for the plant isolates of E. rostratum. The phylogenetic similarity between the clinical and plant-associated E. rostratum isolates and the ability of the clinical isolate to infect plants suggests that a plant pathogenic strain of E. rostratum contaminated the corticosteroid injection fluid and was able to cause systemic disease in the affected patient. This is the first proof that a clinical isolate of E. rostratum is also an effective plant pathogen.

Strategies for the evaluation and selection of potential vaginal probiotics from human sources: an exemplary study

During the last years, the application of probiotics in gynaecological clinical practice has gained increasing relevance regarding therapy and prevention. This trend has also provoked the need for having tailored pharmaceutical preparations containing powerful microbial strains with defined properties. For the development of such preparations, several factors and criteria have to be considered, thereby not only focusing on identity and safety aspects as well as individual properties of the bacterial strains, but also on technological issues, such as stability and targeted release from the preparation. Against this background, this report exemplarily addresses the development procedure of a probiotic bacterial formulation for gynaecological application, covering the search for suitable strains, assessing their microbiological, molecular biological and physiological characterisation, and the selection for their use in clinical trials. In detail, starting with 127 presumptive lactobacilli isolates of vaginal origin, a step-by-step selection of candidate strains meeting special criteria was thoroughly examined, finally leading to a preparation consisting of four individual Lactobacillus strains that possess particular significance in women's urogenital health. Relevant issues and quality criteria of probiotic preparations used in gynecology are addressed and exemplarily introduced.

The effects of different disease-resistant cultivars of banana on rhizosphere microbial communities and enzyme activities

To understand the mechanism of soil microbial ecosystem and biochemical properties in suppressing soilborne plant diseases, the relationship between the soil rhizosphere microbial communities, hydrolase activities, and different disease-resistant cultivars was investigated. There were statistically significant differences in microbial diversity in the rhizosphere soil between the disease-tolerant cultivar Fj01 and susceptible cultivar Baxi. The rhizosphere soil of Fj01 showed a trend of higher microbial diversity than that of Baxi. At the same growth stage, the similar trends of variation in microbial community diversity between the two different cultivars were observed. The bacterial community abundance in rhizosphere soil from the two banana cultivars was quantified by real-time PCR assays. The size of the rhizosphere bacterial population from the Fj01 was significantly larger than that from the Baxi during the growing stage from July to September. The activities of urease and phosphatase were analyzed to study the effects of the two banana cultivars to soil ecosystem functioning. Urease activity was significantly higher in the rhizosphere soil of Fj01 than that of Baxi in the period from July to September. However, phosphatase activity showed no significant difference between the two different rhizosphere soils.

Different selective effects on rhizosphere bacteria exerted by genetically modified versus conventional potato lines

BACKGROUND

In this study, we assessed the actively metabolizing bacteria in the rhizosphere of potato using two potato cultivars, i.e. the genetically-modified (GM) cultivar Modena (having tubers with altered starch content) and the near-isogenic non-GM cultivar Karnico. To achieve our aims, we pulse-labelled plants at EC90 stage with (13)C-CO2 and analysed their rhizosphere microbial communities 24 h, 5 and 12 days following the pulse. In the analyses, phospholipid fatty acid/stable isotope probing (PLFA-SIP) as well as RNA-SIP followed by reverse transcription and PCR-DGGE and clone library analysis, were used to determine the bacterial groups that actively respond to the root-released (13)C labelled carbonaceous compounds.

METHODOLOGY/PRINCIPAL FINDINGS

The PLFA-SIP data revealed major roles of bacteria in the uptake of root-released (13)C carbon, which grossly increased with time. Gram-negative bacteria, including members of the genera Pseudomonas and Burkholderia, were strong accumulators of the (13)C-labeled compounds at the two cultivars, whereas Gram-positive bacteria were lesser responders. PCR-DGGE analysis of cDNA produced from the two cultivar types showed that these had selected different bacterial, alpha- and betaproteobacterial communities at all time points. Moreover, an effect of time was observed, indicating dynamism in the structure of the active bacterial communities. PCR-DGGE as well as clone library analyses revealed that the main bacterial responders at cultivar Karnico were taxonomically affiliated with the genus Pseudomonas, next to Gluconacetobacter and Paracoccus. Cultivar Modena mainly attracted Burkholderia, next to Moraxella-like (Moraxellaceae family) and Sphingomonas types.

CONCLUSIONS/SIGNIFICANCE

Based on the use of Pseudomonas and Burkholderia as proxies for differentially-selected bacterial genera, we conclude that the selective forces exerted by potato cultivar Modena on the active bacterial populations differed from those exerted by cultivar Karnico.

Changes in root bacterial communities associated to two different development stages of canola (Brassica napus L. var oleifera) evaluated through next-generation sequencing technology

Crop production may benefit from plant growth-promoting bacteria. The knowledge on bacterial communities is indispensable in agricultural systems that intend to apply beneficial bacteria to improve plant health and production of crops such as canola. In this work, the diversity of root bacterial communities associated to two different developmental phases of canola (Brassica napus L.) plants was assessed through the application of new generation sequencing technology. Total bacterial DNA was extracted from root samples from two different growth states of canola (rosette and flowering). It could be shown how bacterial communities inside the roots changed with the growing stage of the canola plants. There were differences in the abundance of the genera, family, and even the phyla identified for each sample. While in both root samples Proteobacteria was the most common phylum, at the rosette stage, the most common bacteria belonged to the family Pseudomonadaceae and the genus Pseudomonas, and in the flowering stage, the Xanthomonadaceae family and the genus Xanthomonas dominated the community. This implies in a switch in the predominant bacteria in the different developmental stages of the plant, suggesting that the plant itself interferes with the associated microbial community.

Distinctive bacterial communities in the rhizoplane of four tropical tree species

It is known that the microbial community of the rhizosphere is not only influenced by factors such as root exudates, phenology, and nutrient uptake but also by the plant species. However, studies of bacterial communities associated with tropical rainforest tree root surfaces, or rhizoplane, are lacking. Here, we analyzed the bacterial community of root surfaces of four species of native trees, Agathis borneensis, Dipterocarpus kerrii, Dyera costulata, and Gnetum gnemon, and nearby bulk soils, in a rainforest arboretum in Malaysia, using 454 pyrosequencing of the 16S rRNA gene. The rhizoplane bacterial communities for each of the four tree species sampled clustered separately from one another on an ordination, suggesting that these assemblages are linked to chemical and biological characteristics of the host or possibly to the mycorrhizal fungi present. Bacterial communities of the rhizoplane had various similarities to surrounding bulk soils. Acidobacteria, Alphaproteobacteria, and Betaproteobacteria were dominant in rhizoplane communities and in bulk soils from the same depth (0-10 cm). In contrast, the relative abundance of certain bacterial lineages on the rhizoplane was different from that in bulk soils: Bacteroidetes and Betaproteobacteria, which are known as copiotrophs, were much more abundant in the rhizoplane in comparison to bulk soil. At the genus level, Burkholderia, Acidobacterium, Dyella, and Edaphobacter were more abundant in the rhizoplane. Burkholderia, which are known as both pathogens and mutualists of plants, were especially abundant on the rhizoplane of all tree species sampled. The Burkholderia species present included known mutualists of tropical crops and also known N fixers. The host-specific character of tropical tree rhizoplane bacterial communities may have implications for understanding nutrient cycling, recruitment, and structuring of tree species diversity in tropical forests. Such understanding may prove to be useful in both tropical forestry and conservation.

Polymorphisms within the prnD and pltC genes from pyrrolnitrin and pyoluteorin-producing Pseudomonas and Burkholderia spp

Abstract Pyrrolnitrin (PRN) and pyoluteorin (PLT) are broad-spectrum antibiotics produced by several strains of Pseudomonas and Burkholderia species. Both antibiotics play an important role in the suppression of multiple plant pathogenic fungi. Primers were developed from conserved sequences and amplified prnD and pltC fragments from 18 Pseudomonas and four Burkholderia spp. of worldwide origin that produce either PRN or PLT or both. Subsequent RFLP (restriction fragment length polymorphisms) analysis of the 438-bp pltC fragment showed no polymorphisms among PLT-producing Pseudomonas strains. Polymorphisms within the 786-bp prnD fragment, however, allowed the assessment of the diversity among PRN-producing Pseudomonas and Burkholderia spp. to a level similar to that obtained by three 10-mer primers in random amplified polymorphic DNA analysis. Phylogenetic analysis of 16S rDNA sequences of strains representative of PRN-producing Pseudomonas and Burkholderia species correlated well with their taxonomic status. Phylogenetic relationships inferred from each of the four prn genes and from the complete sequence of the prn biosynthetic locus were similar to 16S rDNA-based phylogeny for most strains, except for Burkholderia pyrrocinia DSM 10685. Both RFLP analysis and comparison of the prn gene sequences showed that B. pyrrocinia DSM 10685 was more closely related to PRN-producing Pseudomonas strains, suggesting that lateral gene transfer may have occurred. Colony hybridization and PCR with PRN- and PLT-specific probes and primers showed that Pseudomonas and Burkholderia spp. harboring the prnD and pltC gene were not present at detectable levels on roots of wheat grown in five agricultural soils collected in The Netherlands, two of them being naturally suppressive to Gaeumannomyces graminis var. tritici. These results suggest that PRN- and PLT-producing Pseudomonas and Burkholderia sp. do not contribute to the natural suppressiveness found in these Dutch take-all decline soils.

Long-term effect of set potential on biocathodes in microbial fuel cells: electrochemical and phylogenetic characterization

The long-term effect of set potential on oxygen reducing biocathodes was investigated in terms of electrochemical and biological characteristics. Three biocathodes were poised at 200, 60 and -100 mV vs. saturated calomel electrode (SCE) for 110 days, including the first 17 days for startup. Electrochemical analyses showed that 60 mV was the optimum potential during long-term operation. The performance of all the biocathodes kept increasing after startup, suggesting a period longer than startup time needed to make potential regulation more effective. The inherent characteristics without oxygen transfer limitation were studied. Different from short-term regulation, the amounts of biomass were similar while the specific electrochemical activity was significantly influenced by potential. Moreover, potential showed a strong selection for cathode bacteria. Clones 98% similar with an uncultured Bacteroidetes bacterium clone CG84 accounted for 75% to 80% of the sequences on the biocathodes that showed higher electrochemical activity (60 and -100 mV).