The plant growth promoting bacterium <Emphasis Type="Italic">Azospirillum brasilense</Emphasis> is vertically transmitted in <Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> (common bean)

Bactrocera dorsalis (Diptera: Tephritidae) is a serious menace to agricultural production worldwide. In order to prevent further damage, it is of paramount important that cost-effective strategies should be developed for their management. Gut bacteria has established diverse relationships with their insect hosts, which could be exploited in pest management programs to improve on control efficiency. In this study, gut bacteria isolates identified by culture dependent technique were incorporated into larval diets in an attempt to understand the roles they play in the development and survival of oriental fruit fly. From our results, the isolated bacteria belonged to four different phyla including the Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. The response of the fly to different gut isolates varied greatly. Diets enriched with Enterococcus phoeniculicola had lower larval developmental duration, higher pupal weight, and an increased percentage survival. On the other hand, diets supplemented with Lactobacillus lactis had negative effects on B. dorsalis development. This study provides clues on how symbiotic bacteria could be exploited in mass rearing for an efficient implementation of the Sterile Insect Technique (SIT) in pest management programs.     

Gut bacterial diversity of farmed sea cucumbers <Emphasis Type="Italic">Apostichopus japonicus</Emphasis> with different growth rates

Farmed sea cucumbers (Apostichopus japonicus) of the same age displayed significantly different body sizes and weights under the same farming conditions. To examine the gut bacterial diversity of sea cucumbers and whether the growth differences between them were related to intestinal microbiota, the bacterial species from intestinal samples of 30 farmed A. japonicus from the same tank (15 large sea cucumbers vs. 15 small sea cucumbers) were characterized based on 16S rRNA gene analysis by means of high throughout sequencing. The results showed that bacterial phylotypes in both sizes of sea cucumbers were closely related to Proteobacteria, Verrucomicrobia, Bacteroidetes, Actinobacteria, Firmicutes, Cyanobacteria, Planctomycete, and Spirochaetes, of which Proteobacteria were predominant (>50%). There were no significant differences in the relative abundances of each bacterial phylotype between the two groups, except for Actinobacteria (P < 0.05). In addition, different species uniquely belonging to all three tested samples in the large group and the small group were found. It was interestingly that Vibrio were absent from both groups. It is likely that the differences in the abundances of Actinobacteria and different species in the two groups may be related to their remarkable disparities in body sizes.     

Grass vs. tree origin of soil organic carbon under different land-use systems in the Brazilian Cerrado

Aims

This study aimed at assessing whether patch type (i.e., under-shrub soil patch and inter-shrub soil patch) has an effect on soil microbes and how different shrub species altered the soil microbes through understanding soil microbial activity, biomass, and community structure.

Methods

We characterized the soil microbes in under-shrub and inter-shrub soil patches in three shrublands (Artemisia ordosica, Salix psammophila, and Caragana microphylla), respectively, in the Mu Us Desert, China, using microbial activity indicators, chloroform fumigation-extraction analysis, and high-throughput 16S rRNA gene sequencing.

Results

Members of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Planctomycetes, Bacteroidetes, Chloroflexi, Firmicutes, and Gemmatimonadetes were dominant. Inter-shrub soil patch differed from under-shrub soil patch in soil bacterial composition, microbial enzyme activity, and biomass, but not in diversity. Soil collected in A. ordosica shrubland exhibited the highest microbial enzyme activity, biomass, and diversity. Shrub species had significant effects on community structure, primarily the relative abundance of Proteobacteria, Actinobacteria, and Bacteroidetes.

Conclusions

The results indicated that both shrub species and patch type had effects on soil microbial communities. In shrub-dominated desert ecosystems, spatial heterogeneity of soil nutrients and moisture might not be the main factors underlying variations in bacterial diversity. The different compositions of microbial communities in various shrublands provide a foundation for further research into the mechanisms of soil organic carbon accumulation.

     

Phylogeny and bioactivity of epiphytic Gram-positive bacteria isolated from three co-occurring antarctic macroalgae

Marine macroalgae are emerging as an untapped source of novel microbial diversity and, therefore, of new bioactive secondary metabolites. This study was aimed at assessing the diversity and antimicrobial activity of the culturable Gram-positive bacteria associated with the surface of three co-occurring Antarctic macroalgae. Specimens of Adenocystis utricularis (brown alga), Iridaea cordata (red alga) and Monostroma hariotii (green alga) were collected from the intertidal zone of King George Island, Antarctica. Gram-positive bacteria were investigated by cultivation-based methods and 16S rRNA gene sequencing, and screened for antimicrobial activity against a panel of pathogenic microorganisms. Isolates were found to belong to 12 families, with a dominance of Microbacteriaceae and Micrococcaceae. Seventeen genera of Actinobacteria and 2 of Firmicutes were cultured from the three macroalgae, containing 29 phylotypes. Three phylotypes within Actinobacteria were regarded as potentially novel species. Sixteen isolates belonging to the genera Agrococcus, Arthrobacter, Micrococcus, Pseudarthrobacter, Pseudonocardia, Sanguibacter, Staphylococcus, Streptomyces and Tessaracoccus exhibited antibiotic activity against at least one of the indicator strains. The bacterial phylotype composition was distinct among the three macroalgae species, suggesting that these macroalgae host species-specific Gram-positive associates. The results highlight the importance of Antarctic macroalgae as a rich source of Gram-positive bacterial diversity and potentially novel species, and a reservoir of bacteria producing biologically active compounds with pharmacological potential.     

Distinctive features of the microbial diversity and the polyketide synthase genes spectrum in the community of the endemic Baikal sponge <Emphasis Type="Italic">Swartschewskia papyracea</Emphasis>

The diversity of the symbiotic community of the endemic Baikal sponge Swartschewskia papyracea was studied, and an analysis of the polyketide synthases genes spectrum in sponge-associated microorganisms was carried out. Six bacterial phyla were detected in the S. papyracea microbiome: Verrucomicrobia, Cyanobacteria, Actinobacteria, Bacteroidetes, Proteobacteria, and Planctomycetes. Unlike the microbial associations of other freshwater sponges, the community under study was dominated by the phylaVerrucomicrobia (42.1%) and Cyanobacteria (17.5%), while the proportion of the Proteobacteria was unusually low (9.7%). In the S. papyracea community metagenome, there were identified 18 polyketide synthases genes fragments, the closest homologues of which included the polyketide synthases of the microorganisms belonging to the bacterial phyla Cyanobacteria, Proteobacteria (classes Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria), and Acidobacteria as well as the eukaryotic algae of the phylum Heterokonta (class Eustigmatophyceae). Polyketide synthase sequences from S. papyracea formed three groups on the phylogenetic tree: a group of hybrid NRPS/PKS complexes, a group of cyanobacterial polyketide synthases, and a group of homologues of the eukaryotic alga Nannochloropsis gaditana. Notably, the identified polyketide synthase genes fragments showed only a 57–88% similarity to the sequences from the databases, which implies the presence of genes controlling the synthesis of the novel, still unstudied, polyketide compounds in the S. papyracea community. It was proposed that the habitat conditions of S. papyracea affect the taxonomic composition of the microorganisms associated with the sponge, including the diversity of the producers of secondary metabolites.     

Halophilic-psychrotrophic bacteria of an Alaskan cryopeg—a model for astrobiology

Cryopegs, lenses of hypersaline unfrozen soil or water within permafrost, are a model for astrobiology, since free water can only be present on cryogenic bodies and planets in the form of brine. In this paper the diversity of aerobic halophilic-psychrotrophic microorganisms from an Alaskan cryopeg (Barrow Cape) were studied and described for the first time. This cryopeg is characterized by a constant subzero temperature (–7°C), high salinity (total mineralization is about 120 g/L) and isolation from external influences for a geologically significant period of time. Our study has revealed a large number of microorganisms capable of growth at low temperature (4°C) in a wide range of salinities from 5 to 250 g/L of NaCl, the latter being 3 times higher than the natural salt concentration of the Alaskan cryopeg. The microorganisms identified are comprised of four major phyla: Actinobacteria (genera Brevibacterium, Citricoccus, Microbacterium), Firmicutes (genus Paenibacillus), Bacteroidetes (genus Sphingobacterium), and Proteobacteria (genus Ochrobactrum).     

Evaluation of microbial population dynamics in the co-composting of cow manure and rice straw using high throughput sequencing analysis

Microbial population dynamics in co-composting of cow manure and rice straw were evaluated using 16S high throughput sequencing technology. Physicochemical factors, including temperature, pH, nitrogen contents, the ratio of carbon and nitrogen, and germination index, were also determined in this study. 16S high throughput sequencing results showed that bacterial community structure and composition significantly varied in each phase of composting. The major phyla included Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria and Planctomycetes, respectively. Bacteroidetes and Proteobacteria were the most abundant phyla in all phases, and Actinobacteria was just dominant in the mesophilic phase, while Firmicutes and Planctomycetes were ubiquitous. At the genus level, Simiduia, Flavobacterium, unclassified Chitinophagaceae and Flexibacter notably changed in each phase of composting. Bacterial community diversity in the mesophilic phase was higher than that in others based on the Shannon–Wiener index and Simpson diversity index. The ratio of carbon and nitrogen and germination index indicated that the co-composting of cow manure and rice straw reached maturation. The result of nitrogen contents showed that nitrogen loss mainly occurred in the thermophilic phase. In addition, the differences in the distributions of key OTUs between in the late thermophilic phase and the cooling and maturation phase were unobvious compared with other phase’s base on the principal component analysis. Redundancy analysis revealed that the changes of nitrogen played a predominant role in the distributions of OTUs during the composting process.     

Fecal Bacterial Composition of Sichuan Snub-Nosed Monkeys (<Emphasis Type="Italic">Rhinopithecus roxellana</Emphasis>)

The intestinal microbiota plays an important role in maintaining the health of its host, including human and nonhuman primates. Little is known about the intestinal bacterial composition of the Sichuan snub-nosed monkey (Rhinopithecus roxellana), which has been classified as Endangered on the International Union for Conservation of Nature Red List since 2003. We evaluated the fecal bacterial compositions of 11 Sichuan snub-nosed monkeys, including six young captive individuals (one sample from each), three adult captive individuals (four samples each), and two adult provisioned free-ranging individuals (four samples each). We also quantified fecal Bacteroides vulgatus, Bifidobacterium spp., and Lactobacillus spp., which are defined as probiotics in humans, using real-time polymerase chain reaction. We identified five major phyla in the collected samples, including Firmicutes (32.4 %), Bacteroidetes (14.7 %), Verrucomicrobia (8.8 %), Actinobacteria (4.4 %), and unclassified microbacteria (39.7 %). Fecal bacteria composition varied with age and different seasons. The fecal bacterial composition of the captive monkeys was less variable than that of provisioned free-ranging monkeys. B. vulgatus amounts were almost 100 times higher in the provisioned free-ranging monkeys (10¹²) than in the captive monkeys (10¹⁰). Our results provide an initial catalogue of gut microbiota in the Sichuan snub-nosed monkey, which helps to enrich our knowledge of gut microbiota in nonhuman primates.     

Exploring the oral microflora of preschool children

The oral cavity is one of the most important and complicated habitats in our body and supports diverse microbial communities. In this study, we aimed to determine the bacterial diversity and composition of various oral micro-niches. Samples were collected from supragingival plaque, saliva, and tongue coating from 10 preschool children (30 samples total). 16S rRNA gene pyrosequencing dataset generated 314,639 clean reads with an average of 10,488 ± 2,787 reads per sample. The phyla Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria were predominant, accounting for more than 90% of the total sequences. We found the highest α diversity, microbial richness, and evenness in plaque, compared with saliva and tongue coating. Plaque was also distinguished from saliva and tongue coating by phylogenetic distances (weighted UniFrac). Taxa with different relative abundances were further identified, confirming the existence of microbial differences across the three niches. Core microbiomes were defined of each niche; however, only a small proportion of operational taxonomic units (8.07%) were shared by the three niches. Coaggregation between Actinomyces spp. and Streptococcus spp. and other correlations among periodontal pathogens, such as Prevotella, Fusobacteria, Capnocytophaga, and Tannerella, were shown by a co-occurrence network. In summary, our study provides a framework of oral microbial communities in the population of preschool children as a baseline for further studies of oral diseases related to microbes.     

Antifouling activity as a function of population variation in <Emphasis Type="Italic">Sargassum vulgare</Emphasis> from the littoral of Rio de Janeiro (Brazil)

The brown seaweed Sargassum vulgare is abundant along the coast of Rio de Janeiro state. An investigation of the spatial variation of antifouling activity was conducted, in which algae were collected at five locations along the coast of Rio de Janeiro during October 2008. Hexane, dichloromethane, methanol and acetone/water extracts were prepared and screened for their bioactivities against the growth of five strains of marine fouling bacteria, five biofilm-associated microphytobenthic strains and attachment of the mussel Perna perna. The most active were the hexane extracts from Bananal algae that inhibited the growth of all microalgae tested; the methanol and dichloromethane extracts from Mar do Norte, which inhibited Vibrio aestuarianus and Pseudoalteromonas elyakovii and the polyphenol extracts from Ilha de Itacuruçá and Bananal that inhibited mussel attachment, respectively, by 64% and 71% compared to controls.     

Isolation and Characterization of Bacterial Species from Ain Mud Volcano,Iran

Along the coastal belt of Makran, on the southeastern margin of Iran, there are several active and inactive mud volcanoes with different morphologies. Ain—an actively bubbling eye-shaped mud pool—is one of these unique geological phenomena. Present study indicates the first overview of the bacterial diversity of this mud volcano obtained by culture techniques. For this purpose, two samples were collected at two different depths of the mud pool and were cultivated on two different nutrient culture media. A total of 13 isolates were randomly chosen for further phenotypic and genotypic characterization. Growth of the isolates occurred at 25–42°C, pH 8–10 and 0–10% NaCl, indicating that most of them were haloalkaliphiles. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the bacterial isolates belonged to three major taxa: Gammaproteobacteria (genera: Marinobacter, Nitrincola, Stentrophomonas), Actinobactera (genera: Kocuria, Brevibacterium, Dietzia) and Firmicutes (genus Planomicrobium). Gammaproteobacteria were the most abundant, following Actinobacteria and Firmicutes. Most of the strains isolated in the present study had the ability to produce extracellular hydrolytic enzymes such as lipases, amylases, proteases and DNases, making them important biotechnologically.     

Leaf-residing <Emphasis Type="Italic">Methylobacterium</Emphasis> species fix nitrogen and promote biomass and seed production in <Emphasis Type="Italic">Jatropha curcas</Emphasis>

Background

Jatropha curcas L. (Jatropha) is a potential biodiesel crop that can be cultivated on marginal land because of its strong tolerance to drought and low soil nutrient content. However, seed yield remains low. To enhance the commercial viability and green index of Jatropha biofuel, a systemic and coordinated approach must be adopted to improve seed oil and biomass productivity. Here, we present our investigations on the Jatropha-associated nitrogen-fixing bacteria with an aim to understand and exploit the unique biology of this plant from the perspective of plant–microbe interactions.

Results

An analysis of 1017 endophytic bacterial isolates derived from different parts of Jatropha revealed that diazotrophs were abundant and diversely distributed into five classes belonging to α, β, γ-Proteobacteria, Actinobacteria and Firmicutes. Methylobacterium species accounted for 69.1 % of endophytic bacterial isolates in leaves and surprisingly, 30.2 % which were able to fix nitrogen that inhabit in leaves. Among the Methylobacterium isolates, strain L2-4 was characterized in detail. Phylogenetically, strain L2-4 is closely related to M. radiotolerans and showed strong molybdenum-iron dependent acetylene reduction (AR) activity in vitro and in planta. Foliar spray of L2-4 led to successful colonization on both leaf surface and in internal tissues of systemic leaves and significantly improved plant height, leaf number, chlorophyll content and stem volume. Importantly, seed production was improved by 222.2 and 96.3 % in plants potted in sterilized and non-sterilized soil, respectively. Seed yield increase was associated with an increase in female–male flower ratio.

Conclusion

The ability of Methylobacterium to fix nitrogen and colonize leaf tissues serves as an important trait for Jatropha. This bacteria–plant interaction may significantly contribute to Jatropha’s tolerance to low soil nutrient content. Strain L2-4 opens a new possibility to improve plant’s nitrogen supply from the leaves and may be exploited to significantly improve the productivity and Green Index of Jatropha biofuel.

     

Diversity of Heterotrophic Halophilic Bacteria Isolated from Coastal Solar Salterns,Bulgaria and Their Ability to Synthesize Bioactive Molecules with Biotechnological Impact

Investigations on the microbial life in several coastal solar salterns have revealed the presence of novel organisms and synthesis of unusual molecules active in extreme conditions which might be useful in different biotechnological industries. Biodiversity of heterotrophic aerobic bacteria isolated from two salterns, Pomorie salterns and Burgas salterns located at Burgas Bay, Black Sea coast, Bulgaria, as well as ability of the isolates to synthesize biotechnologically valuable compounds were investigated. The results revealed high taxonomic and metabolic bacterial diversity—we isolated 20 morphologically different moderately halophilic and two halotolerant strains affiliated with 11 species from eight genera referred to the phyla Proteobacteria, Firmicutes, and Actinobacteria. Gram-negative bacteria belonged to the genera Halomonas, Chromohalobacter, Salinivibrio, Cobetia, and Nesiotobacter, and gram-positive strains were representatives of the genera Virgibacillus, Salinicoccus, and Brevibacterium. All isolates were found to be alkalitolerant, and 41% of them were psychrotolerant. The strains degraded nine of the tested 18 substrates; polygalacturonase, catalase, phytase, and lipase producers were predominant. This is the first reported detection of xanthan lyase, gellan lyase, arabinase, and phytase activities in halophilic bacteria. Nine of the strains belonging to five different genera were found to produce exopolysaccharides (EPS). The highest level of EPS was observed in Chromohalobacter canadensis strain 28. More than a half of the strains displayed antimicrobial activity against one to five test bacteria and yeasts. The present study is the first report on halophilic bacteria isolated from salterns at the Black Sea coast indicating that the investigated area is an untapped resource of halophilic bacteria with biotechnological potential.     

Spatial dynamics of the bacterial community structure in the gastrointestinal tract of red kangaroo (<Emphasis Type="Italic">Macropus rufus</Emphasis>)

The quantification and community of bacteria in the gastrointestinal (GI) tract (stomach, jejunum, ileum, cecum, colon and rectum) of red kangaroos (Macropus rufus) were examined by using real-time PCR and paired-end Illumina sequencing. The quantification of bacteria showed that the number of bacteria in jejunum and rectum was significantly lower than that in colon and cecum (P < 0.05). A total of 1,872,590 sequences was remained after quality-filtering and 50,948 OTUs were identified at the 97 % similarity level. The dominant phyla in the GI tract of red kangaroos were identified as Actinobacteria, Bacteroidetes and Firmicutes. At the level of genus, the samples from different parts of GI tract clustered into three groups: stomach, small intestine (jejunum and ileum) and large intestine (cecum and rectum). Prevotella (29.81 %) was the most dominant genus in the stomach and significantly (P < 0.05) higher than that in other parts of GI tract. In the small intestine, Bifidobacterium (33.04, 12.14 %) and Streptococcus (22.90, 19.16 %) were dominant genera. Unclassified Ruminococcaceae was the most dominant family in large intestine and the total relative abundance of unclassified bacteria was above 50 %. In identified genera, Dorea was the most important variable to discriminate large intestine and it was significantly higher in cecum than in stomach, small intestine and colon (P < 0.05). Bifidobacterium (21.89 %) was the only dominant genus in colon. Future work on culture in vitro and genome sequencing of those unidentified bacteria might give us insight into the function of these microorganisms in the GI tract. In addition, the comparison of the bacterial community in the foregut of kangaroos and other herbivores and the rumen might give us insight into the mechanism of fiber degradation and help us exploit approaches to improve the feed efficiency and subsequently, reduce the methane emission from herbivores.     

Isolation of antibiotic resistance bacterial strains from Eastern Siberia permafrost sediments

A collection of bacterial antibiotic resistance strains isolated from arctic permafrost subsoil sediments of various age and genesis was created. The collection included approximately 100 strains of Gram-positive (Firmicutes, Arthrobacter) and Gram-negative bacteria (Bacteroidetes, γ-Proteobacteria, and α-Proteobacteria) resistant to aminoglycoside antibiotics (gentamicin, kanamycin, and streptomycin), chloramphenicol and tetracycline. Antibiotic resistance spectra were shown to differ in Gram-positive and Gram-negative bacteria. Multidrug resistance strains were found for the first time in ancient bacteria. In studies of the molecular nature of determinants for streptomycin resistance, determinants of the two types were detected: strA-strB genes coding for aminoglycoside phosphotransferases and genes aadA encoding aminoglycoside adenylyltransferases. These genes proved to be highly homologous to those of contemporary bacteria.     

Bacteriological analysis of saliva from partially or fully engorged female adult <Emphasis Type="Italic">Rhipicephalus microplus</Emphasis> by next-generation sequencing

Tick-borne diseases are a major epidemiological problem worldwide. The aim of this study was to investigate the bacterial composition of saliva obtained from engorged adult Rhipicephalus microplus females. Saliva samples collected from partially or fully engorged adult female ticks were analysed using an ultra-high-throughput Illumina HiSeq 2500 sequencing system. To elucidate the possible routes of bacterial transmission, the bacterial flora from whole ticks were also investigated. Proteobacteria, Firmicutes, and Actinobacteria were the predominant phyla in all samples, and Acinetobacter, Rickettsia, Escherichia and Coxiella were the major genera. Microbial diversity in saliva samples from partially engorged ticks was more complex than that of samples from fully engorged individuals. The comparison of saliva and whole-tick samples suggests that bacteria in saliva also colonize the tick’s body. We believe that some bacterial genera, such as Dermacoccus, Achromia, SMB53, Sutterella, Providencia, Mycoplana, Oscillospira, and Agrobacterium, were found and reported in ticks for the first time. The Coxiella and Rickettsia detected in this study might be tick-borne pathogens, suggesting health risks associated with exposure to R. microplus in humans and animals. These findings may serve as the basis for developing strategies to control ticks and tick-borne diseases.     

The first case of disease of the sponge <Emphasis Type="Italic">Lubomirskia baicalensis</Emphasis>: Investigation of its microbiome

The first metagenomic analysis of the microbiome of the first sample of diseased endemic sponge Lubomirskia baicalensis (Pallas, 1771) from Lake Baikal and the comparison of the results with data published earlier on the microbiome of healthy sponges were carried out. Essential changes in the composition and structure of the microbial community were detected in the diseased individual possessing an uncharacteristic pink coloring. Cyanobacteria were predominant in the community, the fraction of the representatives of Verrucomicrobia was increased. The diversity and number of eukaryotic algae, as well as of representatives of Bacteroidetes, Proteobacteria, Actinobacteria, and Planctomycetes, were decreased. A wide range of minor phyla were eliminated. The factors affecting the composition of symbiotic communities in sponges were considered. It was supposed that changes in the structure of symbiotic communities resulting in mass disease and death could be caused by an increase in the methane concentration in the water column of Lake Baikal.     

Microbial community associated with <Emphasis Type="Italic">Thioploca</Emphasis> sp. sheaths in the area of the posolsk bank methane seep,southern baikal

Bacterial mats formed by a colorless sulfur bacterium Thioploca sp. in the area of the Posolsk Bank cold methane seep (southern Baikal) were studied using electron microscopy and phylogenetic analysis. Morphologically the bacteria were identified as Thioploca ingrica. Confocal microscopy of DAPI-stained samples revealed numerous rod-shaped, filamentous, and spiral microorganisms in the sheaths, as well as inside and between the trichomes. Transmission electron microscopy revealed nonvacuolated bacteria and small cells without cell envelopes within the sheath. Bacteria with pronounced intracytoplasmic membranes characteristic of type I methanotrophs were observed at the outer side of the sheath. Based on analysis of the 16S rRNA gene sequences, the following phyla were identified in the sheath community: Bacteroidetes, Nitrospira, Chloroflexi, Planctomycetes, Verrucomicrobia, γ-, and δ-Proteobacteria, Euryarchaeota, Crenarchaeota, and Thaumarchaeota, as well as anammox bacteria. A hypothetical scheme of matter flows in the Lake Baikal bacterial mats was proposed based on the data on metabolism of the cultured homologues.     

Selection for novel,acid-tolerant <Emphasis Type="Italic">Desulfovibrio</Emphasis> spp. from a closed Transbaikal mine site in a temporal pH-gradient bioreactor

Almost all the known isolates of acidophilic or acid-tolerant sulphate-reducing bacteria (SRB) belong to the spore-forming genus Desulfosporosinus in the Firmicutes. The objective of this study was to isolate acidophilic/acid-tolerant members of the genus Desulfovibrio belonging to deltaproteobacterial SRB. The sample material originated from microbial mat biomass submerged in mine water and was enriched for sulphate reducers by cultivation in anaerobic medium with lactate as an electron donor. A stirred tank bioreactor with the same medium composition was inoculated with the sulphidogenic enrichment. The bioreactor was operated with a temporal pH gradient, changing daily, from an initial pH of 7.3 to a final pH of 3.7. Among the bacteria in the bioreactor culture, Desulfovibrio was the only SRB group retrieved from the bioreactor consortium as observed by 16S rRNA-targeted denaturing gradient gel electrophoresis. Moderately acidophilic/acid-tolerant isolates belonged to Desulfovibrio aerotolerans-Desulfovibrio carbinophilus-Desulfovibrio magneticus and Desulfovibrio idahonensis-Desulfovibrio mexicanus clades within the genus Desulfovibrio. A moderately acidophilic strain, Desulfovibrio sp. VK (pH optimum 5.7) and acid-tolerant Desulfovibrio sp. ED (pH optimum 6.6) dominated in the bioreactor consortium at different time points and were isolated in pure culture.     

Diversity of endophytic fungal and bacterial communities in <Emphasis Type="Italic">Ilex paraguariensis</Emphasis> grown under field conditions

The composition and diversity of the endophytic community associated with yerba mate (Ilex paraguariensis) was investigated using culture-depending methods. Fungi were identified based on their micromorphological characteristics and internal transcribed spacer rDNA sequence analysis; for bacteria 16S rDNA sequence analysis was used. Fungal and bacterial diversity did not show significant differences between organ age. The highest fungal diversity was registered during fall season and the lowest in winter. Bacterial diversity was higher in stems and increased from summer to winter, in contrast with leaves, which decreased. The most frequently isolated fungus was Fusarium, followed by Colletotrichum; they were both present in all the sampling seasons and organ types assayed. Actinobacteria represented 57.5 % of all bacterial isolates. The most dominant bacterial taxa were Curtobacterium and Microbacterium. Other bacteria frequently found were Methylobacterium, Sphingomonas, Herbiconiux and Bacillus. Nitrogen fixation and phosphate solubilization activity, ACC deaminase production and antagonism against plant fungal pathogens were assayed in endophytic bacterial strains. In the case of fungi, strains of Trichoderma, Penicillium and Aspergillus were assayed for antagonism against pathogenic Fusarium sp. All microbial isolates assayed showed at least one growth promoting activity. Strains of Bacillus, Pantoea, Curtobacterium, Methylobacterium, Brevundimonas and Paenibacillus had at least two growth-promoting activities, and Bacillus, Paenibacillus and the three endophytic fungi showed high antagonistic activity against Fusarium sp. In this work we have made a wide study of the culturable endophytic community within yerba mate plants and found that several microbial isolates could be considered as potential inoculants useful for improving yerba mate production.