Microarray Analysis of Microbiota of Gingival Lesions in Noma Patients

Noma (cancrum oris) is a gangrenous disease of unknown etiology affecting the maxillo-facial region of young children in extremely limited resource countries. In an attempt to better understand the microbiological events occurring during this disease, we used phylogenetic and low-density microarrays targeting the 16S rRNA gene to characterize the gingival flora of acute noma and acute necrotizing gingivitis (ANG) lesions, and compared them to healthy control subjects of the same geographical and social background. Our observations raise doubts about Fusobacterium necrophorum, a previously suspected causative agent of noma, as this species was not associated with noma lesions. Various oral pathogens were more abundant in noma lesions, notably Atopobium spp., Prevotella intermedia, Peptostreptococcus spp., Streptococcus pyogenes and Streptococcus anginosus. On the other hand, pathogens associated with periodontal diseases such as Aggregatibacter actinomycetemcomitans, Capnocytophaga spp., Porphyromonas spp. and Fusobacteriales were more abundant in healthy controls. Importantly, the overall loss of bacterial diversity observed in noma samples as well as its homology to that of ANG microbiota supports the hypothesis that ANG might be the immediate step preceding noma.     

Bacterial diversity in oral samples of children in niger with acute noma, acute necrotizing gingivitis, and healthy controls

Background

Noma is a gangrenous disease that leads to severe disfigurement of the face with high morbidity and mortality, but its etiology remains unknown. Young children in developing countries are almost exclusively affected. The purpose of the study was to record and compare bacterial diversity in oral samples from children with or without acute noma or acute necrotizing gingivitis from a defined geographical region in Niger by culture-independent molecular methods.

Methods and Principal Findings

Gingival samples from 23 healthy children, nine children with acute necrotizing gingivitis, and 23 children with acute noma (both healthy and diseased oral sites) were amplified using “universal” PCR primers for the 16 S rRNA gene and pooled according to category (noma, healthy, or acute necrotizing gingivitis), gender, and site status (diseased or control site). Seven libraries were generated. A total of 1237 partial 16 S rRNA sequences representing 339 bacterial species or phylotypes at a 98–99% identity level were obtained. Analysis of bacterial composition and frequency showed that diseased (noma or acute necrotizing gingivitis) and healthy site bacterial communities are composed of similar bacteria, but differ in the prevalence of a limited group of phylotypes. Large increases in counts of Prevotella intermedia and members of the Peptostreptococcus genus are associated with disease. In contrast, no clear-cut differences were found between noma and non-noma libraries.

Conclusions

Similarities between acute necrotizing gingivitis and noma samples support the hypothesis that the disease could evolve from acute necrotizing gingivitis in certain children for reasons still to be elucidated. This study revealed oral microbiological patterns associated with noma and acute necrotizing gingivitis, but no evidence was found for a specific infection-triggering agent.     

Composition and activity of rhizosphere microbial communities associated with healthy and diseased greenhouse tomatoes

Aims

The goal of this study was to investigate the structure and functional potential of microbial communities associated with healthy and diseased tomato rhizospheres.

Methods

Composition changes in the bacterial communities inhabiting the rhizospheric soil and roots of tomato plants were detected using 454 pyrosequencing. Microbial functional diversity was investigated with BIOLOG technology.

Results

There were significant shifts in the microbial composition of diseased samples compared with healthy samples, which had the highest bacterial diversity. The predominant phylum in both diseased and healthy samples was Proteobacteria, which accounted for 35.7–97.4 % of species. The class Gammaproteobacteria was more abundant in healthy than in diseased samples, while the Alphaproteobacteria and Betaproteobacteria were more abundant in diseased samples. The proportions of pathogenic Ralstonia solanacearum and Actinobacteria species were also elevated in diseased samples. The proportions of the various bacterial populations showed a similar trend both in rhizosphere soil and plant roots in diseased versus disease-free samples, indicating that pathogen infection altered the composition of bacterial communities in both plant and soil samples. In terms of microbial activity, functional diversity was suppressed in diseased soil samples. Soil enzyme activity, including urease, alkaline phosphatase and catalase activity, also declined.

Conclusions

This is the first report that provides evidence that R. solanacearum infection elicits shifts in the composition and functional potential of microbial communities in a continuous-cropping tomato operation.     

Changes in Cell Membrane Permeability in Sunflower Hypocotyls Infected with Sclerotinia sclerotiorum

Influx and efflux of water and urea and electrolyte leakage are less for sunflower (Helianthus annuus) hypocotyl sections above lesions caused by Sclerotinia sclerotiorum than for those from healthy plants. Urea uptake by sections above lesions is reduced (celery, squash, and tomato) or unchanged (bean) in other hosts after Sclerotinia infection. Efflux of urea from sunflower hypocotyls is biphasic, suggesting diffusion in series from two cellular compartments (cytoplasm and vacuole). Efflux during the fast phase was 7 to 20 times greater than that during the slow phase. No difference was noted in urea efflux from healthy and diseased tissues during the slow phase. However, efflux during the fast phase from diseased tissues was slower than from healthy tissues, suggesting that the increased resistance to diffusion of urea in host cells above lesions resides in the plasmalemma. Water movement across cell membranes of healthy and diseased sunflower hypocotyls was reduced when tissues were treated with p-hydroxymercuribenzoate.     

Microbiological assessment of a disease outbreak on corals from Magnetic Island (Great Barrier Reef, Australia)

Unusual disease lesions were observed in Montipora corals on the fringing reef of Magnetic Island (Great Barrier Reef, Australia) following a period of high water temperature in early January 2002. Tissue death in Montipora spp. appeared as a black layer that spread rapidly across the colony surface, though this appeared as the final phase of disease progression (with three previous disease phases now identified, S. Anthony, unpublished). Culture and molecular-based microbial analysis of this layer did not identify a likely microbial pathogen. Despite this, DNA sequencing of microbial 16S rDNA indicated a shift in the bacterial population associated with affected coral tissue. A clone library of the healthy coral sample predominantly contained sequences within the -Proteobacteria. A disease coral sample representing the margin of the black lesion and healthy coral tissue was dominated by sequences, which demonstrated low sequence identity to a range of -Proteobacteria, -Proteobacteria and cyanobacteria. The microbes identified in the diseased Montipora spp. samples are likely to be opportunistic rather than the causative agent of the observed lesion. Studies are in progress to further characterise the ecology of this disease and describe the potential microbial pathogen(s).     

Electricity generation using chocolate industry wastewater and its treatment in activated sludge based microbial fuel cell and analysis of developed microbial community in the anode chamber

Feasibility of using chocolate industry wastewater as a substrate for electricity generation using activated sludge as a source of microorganisms was investigated in two-chambered microbial fuel cell. The maximum current generated with membrane and salt bridge MFCs was 3.02 and 2.3 A/m², respectively, at 100 Ω external resistance, whereas the maximum current generated in glucose powered MFC was 3.1 A/m². The use of chocolate industry wastewater in cathode chamber was promising with 4.1 mA current output. Significant reduction in COD, BOD, total solids and total dissolved solids of wastewater by 75%, 65%, 68%, 50%, respectively, indicated effective wastewater treatment in batch experiments. The 16S rDNA analysis of anode biofilm and suspended cells revealed predominance of β-Proteobacteria clones with 50.6% followed by unclassified bacteria (9.9%), α-Proteobacteria (9.1%), other Proteobacteria (9%), Planctomycetes (5.8%), Firmicutes (4.9%), Nitrospora (3.3%), Spirochaetes (3.3%), Bacteroides (2.4%) and γ-Proteobacteria (0.8%). Diverse bacterial groups represented as members of the anode chamber community.     

Bacterial phylogenetic diversity in a Spartina marsh in China

The bacterial phylogenetic diversities of the bacterial communities in the salt marsh colonized by Spartina alterniflora (SA) and uncultured marsh (UM) along the Yellow Sea of China were analyzed based on the 16S rDNA PCR techniques. Two libraries containing 251 clones of 16S rRNA genes from the Spartina colonized marsh and 283 from UM were constructed by PCR using a bacteria-specific primer 8f and the common primer 1542r. Forty-seven clones from SA and 55 from UM were selected for partial sequencing. A phylogenetic tree was constructed by the alignment analysis of the total environmental DNA sequences. Clones were clustered into 8 divisions of bacteria: (1) Proteobacteria containing 12 genera in beta, gamma, delta and epsilon subdivision; (2) Bacteroidetes containing 7 genera; (3) Planctomycetes containing 2 genera; (4) Firmicutes containing 1 genus; (5) Spirochaetes containing 1 genus; (6) Acidobacteria containing 1 genus; (7) Actinobacteria containing 1 genus; and (8) BRC1 containing 1 genus, as well as 3 groups of bacteria that could not be clustered into any recognized bacterial divisions or candidate divisions. BLAST searches of the GenBank database confirmed that 79.7% of the clones in the two libraries were closely related to the 16S rDNA sequences of the uncultured bacteria with the similarity ≥90%. Among them, Proteobacteria (36.7% and 54.4% of the total clones from the SA and UM libraries, respectively) and Bacteroidetes (30.0% and 18.3%, respectively) are two dominant groups in both the sites. However, some phyla, such as Firmicutes and Actinobacteria, were found at SA site but not at UM site, and vice versa, some phyla, such as Spirochaetes and BRC1, were found at UM, but not at SA. Moreover, the dominant species in each phylum were varied, dependent on whether or not the marsh was colonized by Spartina. For instance, in Bacteroidete, 44.4% clones at SA library were affiliated to Gelidibacter, but 32.7% clones were affiliated to Flexibacter at UM library. In Proteobacteria, the clones at UM library affiliated to δ, γ, ? and β-subdivisions were 38.8%, 34.7%, 23.5% and 3.1%, respectively, but at SA library were 30.3%, 47.0%, 13.6% and 9.1%, correspondingly. These results indicated that the bacterial diversity in the salt marsh along the Yellow Sea of China was greatly changed after Spartina colonization.     

Effect of propofol on oxidative stress status in erythrocytes from dogs under general anaesthesia

Background

Piglets are born with eight sharp teeth that during nursing can cause facial lesions on littermates and teat lesions on the sow. Teeth grinding in piglets is therefore often practiced to reduce these lesions. The aim of this study was to assess the consequences of grinding piglet teeth in regard to the occurrence of lesions. In this study the piglets' teeth were grinded in 28 litters, and in 36 litters the piglets' teeth were kept intact. Twice, one time during the first week and one time during the second week after birth facial lesions of the piglets were scored and the teats of the sows were examined for lesions. The facial lesion score accounted for the amount and severity of lesions. The individual observations on piglets in the litter were synthesized in a litter facial lesion score.

Findings

69.8% and 43.5% of the piglets had facial lesions in week 1 and week 2 respectively. The effect of treatment was not significant on litter facial lesion score. The litter facial lesion score was higher in week 1 than in week 2 (p < 0.001) and higher in large litters (p = 0.003) than in small litters. Mortality between week 1 and week 2 was higher in litters with intact teeth (p = 0.02). Sow teat lesions only occurred if litters had intact teeth.

Conclusions

According to our results teeth grinding is only justifiable in large litters.     

Angiotensin II Induced Cardiac Dysfunction on a Chip

In vitro disease models offer the ability to study specific systemic features in isolation to better understand underlying mechanisms that lead to dysfunction. Here, we present a cardiac dysfunction model using angiotensin II (ANG II) to elicit pathological responses in a heart-on-a-chip platform that recapitulates native laminar cardiac tissue structure. Our platform, composed of arrays of muscular thin films (MTF), allows for functional comparisons of healthy and diseased tissues by tracking film deflections resulting from contracting tissues. To test our model, we measured gene expression profiles, morphological remodeling, calcium transients, and contractile stress generation in response to ANG II exposure and compared against previous experimental and clinical results. We found that ANG II induced pathological gene expression profiles including over-expression of natriuretic peptide B, Rho GTPase 1, and T-type calcium channels. ANG II exposure also increased proarrhythmic early after depolarization events and significantly reduced peak systolic stresses. Although ANG II has been shown to induce structural remodeling, we control tissue architecture via microcontact printing, and show pathological genetic profiles and functional impairment precede significant morphological changes. We assert that our in vitro model is a useful tool for evaluating tissue health and can serve as a platform for studying disease mechanisms and identifying novel therapeutics.     

Acute necrotic stomatitis (noma) associated with methicillin-resistant Staphylococcus aureus infection in a newly acquired rhesus macaque (Macaca mulatta)

Backgroud A newly acquired rhesus macaque was suffering from rapid destruction of the left cheek caused by necrotizing stomatitis. Methods To restore reconstructive surgery and intensive care with antibiotics, wound protection, wound healing agents, and debridement were applied. Results Staphylococcus aureus and Enterococcus faecalis were isolated from the culture of the lesion, and the antibiotic susceptibility test revealed methicillin‐resistant Staphylococcus aureus infection. Vancomycin and ampicillin‐sulbactam effectively treated the bacterial infections, and reconstructive surgery was performed once the infection was cleared. Topical application of recombinant human epidermal growth factor (rhEGF) was useful to treat exposed wound of the noma lesion. Conclusions Simian noma associated with methicillin‐resistant Staphylococcus aureus (MRSA) had not previously been reported in non‐human primates. Although noma associated with MRSA is hard to cure because of its rapid and destructive progress, the aggressive therapy used in this study led to the successful resolution of an acute necrotic stomatitis lesion in a rhesus macaque.     

Fungi associated with strawberry root rot in Illinois

A qualitative and quantitative study of the fungi associated with apparently healthy and root rot-diseased strawberry main roots was made during a 1-year period. Eighty-one genera were isolated from lesions and stele segments of diseased roots, and tips and segments 5–6 cm from the tip of apparently healthy roots. A diverse mycoflora was isolated from each segment of the root. However, each segment had a typical dominant mycoflora, indicating that a changing mycoflora is associated with the root as it passes from a healthy to a diseased condition.Pythium spp. andRhizoctonia Spp. accounted for 25.09 and 5.67 percent, respectively, of the isolates from Surecrop lesions, and 4.96 and 25.92 percent, respectively, of the isolates from Cyclone lesions.     

A Cross-Sectional Study of ‘Yaws’ in Districts of Ghana Which Have Previously Undertaken Azithromycin Mass Drug Administration for Trachoma Control

Yaws, caused by Treponema pallidum ssp. pertenue, is reportedly endemic in Ghana. Mass distribution of azithromycin is now the cornerstone of the WHO yaws eradication campaign. Mass distribution of azithromycin at a lower target dose was previously undertaken in two regions of Ghana for the control of trachoma. Ongoing reporting of yaws raises the possibility that resistance may have emerged in T. pallidum pertenue, or that alternative infections may be responsible for some of the reported cases. We conducted a cross-sectional survey in thirty communities in two districts of Ghana where MDA for trachoma had previously been conducted. Children aged 5–17 years with ulcerative lesions compatible with yaws were enrolled. Samples for treponemal serology and lesion PCR were collected from all children. 90 children with 98 lesions were enrolled. Syphilis serology was negative in all of them. PCR for T. pallidum ssp pertenue was negative in all children, but Haemophilus ducreyi DNA was detected in 9 lesions. In these communities, previously treated for trachoma, we found no evidence of ongoing transmission of yaws. H. ducreyi was associated with a proportion of skin lesions, but the majority of lesions remain unexplained. Integration of diagnostic testing into both pre and post-MDA surveillance systems is required to better inform yaws control programmes.     

Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing

Periodontitis has a polymicrobial etiology within the framework of a complex microbial ecosystem. With advances in sequencing technologies, comprehensive studies to elucidate bacterial community differences have recently become possible. We used 454 sequencing of 16S rRNA genes to compare subgingival bacterial communities from 29 periodontally healthy controls and 29 subjects with chronic periodontitis. Amplicons from both the V1-2 and V4 regions of the 16S gene were sequenced, yielding 1 393 579 sequences. They were identified by BLAST against a curated oral 16S database, and mapped to 16 phyla, 106 genera, and 596 species. 81% of sequences could be mapped to cultivated species. Differences between health- and periodontitis-associated bacterial communities were observed at all phylogenetic levels, and UniFrac and principal coordinates analysis showed distinct community profiles in health and disease. Community diversity was higher in disease, and 123 species were identified that were significantly more abundant in disease, and 53 in health. Spirochaetes, Synergistetes and Bacteroidetes were more abundant in disease, whereas the Proteobacteria were found at higher levels in healthy controls. Within the phylum Firmicutes, the class Bacilli was health-associated, whereas the Clostridia, Negativicutes and Erysipelotrichia were associated with disease. These results implicate a number of taxa that will be targets for future research. Some, such as Filifactor alocis and many Spirochetes were represented by a large fraction of sequences as compared with previously identified targets. Elucidation of these differences in community composition provides a basis for further understanding the pathogenesis of periodontitis.     

Persistence, Transmission, and Virulence Characteristics of Aeromonas Strains in a Duckweed Aquaculture-Based Hospital Sewage Water Recycling Plant in Bangladesh

The persistence and transmission of Aeromonas in a duckweed aquaculture-based hospital sewage water treatment plant in Bangladesh was studied. A total of 670 samples from different sites of the hospital sewage water treatment plant, from feces of hospitalized children suffering from diarrhea, from environmental control ponds, and from feces of healthy humans were collected over a period of three years. In total, 1,315 presumptive Aeromonas isolates were biochemically typed by the PhenePlate rapid screening system (PhP-AE). A selection of 90 representative isolates was further analyzed with PhenePlate (PhP) extended typing (PhP-48), fatty acid methyl ester analysis, and amplified fragment length polymorphism (AFLP) fingerprinting. In addition, the prevalence of the putative virulence factors hemolysin and cytotoxin and the presence of the cytolytic enterotoxin gene (AHCYTOEN) were analyzed. Aeromonas was found at all sites of the treatment plant, in 40% of the samples from environmental control ponds, in 8.5% of the samples from hospitalized children suffering from diarrhea, and in 3.5% of samples from healthy humans. A significantly high number of Aeromonas bacteria was found in duckweed, which indicates that duckweed may serve as a reservoir for these bacteria. PhP-AE typing allowed identification of more than 192 distinct PhP types, of which 18 major PhP types (MTs) were found in multiple sites and during several occasions. AFLP fingerprinting revealed the prevalence of genotypically indistinguishable Aeromonas isolates among certain PhP MTs recovered from different sampling occasions and/or at multiple sites. Hemolytic and cytotoxic activities were observed in 43% of the tested strains, whereas 29% possessed the cytolytic enterotoxin gene AHCYTOEN. Collectively, two specific MTs associated with diarrhea were shown to exhibit high cytotoxicity. Furthermore, all tested isolates of these major types were positive for the cytolytic enterotoxin gene. In conclusion, our data indicate that certain phenotypically and genotypically stable clonal lineages of Aeromonas have persisted in the treatment system for a prolonged period and might spread from the hospitalized children suffering from diarrhea to fish produced for human consumption through the sewage water treatment system.     

Microbial diversity in uterus of healthy and metritic postpartum Holstein dairy cows

Clone library of bacterial 16S rRNA gene was constructed to evaluate the bacterial diversity and community structure of uterus samples obtained from three postpartum healthy cows and three metritic cows on days 10 and 40. Sequences were assigned to five major groups (Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, and Tenericutes) and to an uncultured group. On day 10, Bacteroidetes, Firmicutes, and Fusobacteria were the dominant group both in healthy and metritic cows. On day 40, the major sequences were affiliated with Bacteroidetes, Firmicutes, Tenericutes, and Proteobacteria. Tenericutes (Ureaplasma diversum) were revealed only from healthy cows, while Proteobacteria (Histophilus somni) were found only from metritic cows. Quantitative PCR revealed that metritic cows on day 10 showed higher value of total bacteria, Bacteroidetes, Peptostreptococcus, and Fusobacterium compared with healthy cows, while only a higher value of Fusobacterium spp. was observed from the metritic cows on day 40 compared with that from healthy cows (P?<?0.05). Our data indicates that great difference in the uterine bacterial community in both phyla level and species level exists between healthy and metritic postpartum cows, and dynamic changes in bacterial community occur over time.     

Pro- versus anti-inflammatory cytokine profile in African children with acute oro-facial noma (cancrum oris, noma)

Fresh noma is a severe orofacial necrosis with an astonishingly rapid development. It is seen mainly in malnourished children less than 4 years old from developing countries. Cytokines play a central role in oral mucosal inflammation. We therefore studied the relevance of circulating cytokines to noma, and the key microorganisms associated with the lesion. Nigerian village children with acute noma (n=68) and their neighborhood village (n=63) as well as urban (n=45) counterparts of comparable age and free of overt infections were evaluated for serum cytokine levels by ELISA. Oral bacteria were studied by polymerase chain reaction. Evaluation of random cases of the village and noma children showed marked depletion (p<0.05 or 0.001) of the plasma antioxidant micronutrients (retinol, ascorbic acid, zinc) as well as albumin and blood hemoglobin in the latter, relative to the former group. Concentrations of the circulating, pro-inflammatory cytokines (IL-18, IL-6, IL-12, IL-8, IFN-gamma) and the soluble inhibitors (TNFR-p55, TNFR-p75 and IL-1ra) were significantly higher (p<0.01 or 0.001) in noma children than in the healthy urban children, but less so when compared to their neighborhood village counterparts. The increase in levels of the anti-inflammatory/regulatory cytokines (IL-4, IL-10 and TGF-beta) was less marked relative to the pro-inflammatory cytokines. Bacteria observed at the highest frequencies in noma lesions were P. intermedia (83%), T. forsythensis (83%), P. gingivalis (50%), C. rectus (50%) and T. denticola (50%). We conclude that noma is an immunopathological response to potent bacterial factors resulting in uncontrolled production of cytokines and possibly other, still unknown, inflammatory mediators.     

Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana

Cryptocercus punctulatus and Parasphaeria boleiriana are two distantly related xylophagous and subsocial cockroaches. Cryptocercus is related to termites. Xylophagous cockroaches and termites are excellent model organisms for studying the symbiotic relationship between the insect and their microbiota. In this study, high-throughput 454 pyrosequencing of 16S rRNA was used to investigate the diversity of metagenomic gut communities of C. punctulatus and P. boleiriana, and thereby to identify possible shifts in symbiont allegiances during cockroaches evolution. Our results revealed that the hindgut prokaryotic communities of both xylophagous cockroaches are dominated by members of four Bacteria phyla: Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Other identified phyla were Spirochaetes, Planctomycetes, candidatus Saccharibacteria (formerly TM7), and Acidobacteria, each of which represented 1–2% of the total population detected. Community similarity based on phylogenetic relatedness by unweighted UniFrac analyses indicated that the composition of the bacterial community in the two species was significantly different (P < 0.05). Phylogenetic analysis based on the characterized clusters of Bacteroidetes, Spirochaetes, and Deltaproteobacteria showed that many OTUs present in both cockroach species clustered with sequences previously described in termites and other cockroaches, but not with those from other animals or environments. These results suggest that, during their evolution, those cockroaches conserved several bacterial communities from the microbiota of a common ancestor. The ecological stability of those microbial communities may imply the important functional role for the survival of the host of providing nutrients in appropriate quantities and balance.     

Microbiota of Initial Periodontitis in Adults

This paper reviews our recent studies of the microbiota and host response of initial periodontitis. Understanding the initial stages of periodontitis will allow appropriate early treatment and prevention strategies. Out studies aimed to determine the major bacterial species that differentiated initial periodontitis from health, and evaluate whether subjects with initial periodontitis differed in serum IgG reactivity to putative initial periodontitis pathogens compared with healthy subjects. Initial periodontitis was characterized clinically using longitudinal periodontial attachment level measurements. Progressing periodontal loss was detected at interproximal (initial periodontitis), and buccal (progressing recession) locations from the study population of minimally periodontally diseased subjects. Initial periodontitis was characterized microbiologically by elevated proportions of Bacteroides forsythus, Selenomonas noxia and Campylobacter rectus when compared with non-periodontitis sites. The immunological checkerboard assay did not detect differences in serum IgG reactivity among healthy, gingivitis or initial periodontitis subjects, or changes in reactivity co-incident with detection of initial peridontitis. Clinical, microbiological and immunological characterization of initial periodontitis was consistent with infection-associated Gram-negative anaerobic periodontal species. Progressing recession sites were colonized byActinomyces and Streptococcus species, as were healthy sites. Progressing recession sites demonstrated periodontal loss that appeared unrelated to infection and appeared to be consistent with a traumatic tooth brushing etiology. Different types of lesions will require different approaches to therapy and prevention.     

Phylogenetic Analysis and Metabolic Potential of Microbial Communities in an Industrial Bagasse Collection Site

Industrial bagasse collection sites at sugar mills are an important resource for biomass-based industries and represent a unique ecological niche in lignocellulose degradation. In this study, microbial community structures at regions with varying microenvironmental conditions contained within a bagasse collection site were explored using tagged 16S rRNA gene pyrosequencing. Overall, remarkable differences in microbial community structures were found in aerobic surface and oxygen-limited interior regions of the pile. A variety of Alphaproteobacteria and Gammaproteobacteria represented the majority of bacteria in the aerobic upper-pile regions with the predominance of acetic acid bacteria towards the outer surface. Diverse Proteobacteria, Bacteroidetes, and Acidobacteria represented the predominant phyla at the exterior soil-contact pile base with an increasing abundance of anaerobic Spirochaetes with the increasing depth, where it shared similar community structures to that in the open-field soil from decomposed bagasse. Using complementary shotgun pyrosequencing, a variety of genes encoding various glycosyl hydrolases targeting cellulose and hemicellulose degradation were identified in the oxygen-limited interior pile base. Most were relevant to orders Clostridiales, Bacteroidales, Sphingobacteriales, and Cytophagales, suggesting their role in lignocellulose degradation in this region, as evidenced by the decrease in cellulose and respective increase in lignin fractions of the biomass. Partial carbon flux in the anoxic region was metabolized through mixed methanogenesis pathways as suggested by the annotated functional genes in methane synthesis. This study gives insights into native microbial community structures and functions in this unique lignocellulose degrading environment and provides the basis for controlling microbial processes important for utilization of bagasse in bio-industries.     

Growth and Phylogenetic Properties of Novel Bacteria Belonging to the Epsilon Subdivision of the Proteobacteria Enriched from Alvinella pompejana and Deep-Sea Hydrothermal Vents

Recent molecular characterizations of microbial communities from deep-sea hydrothermal sites indicate the predominance of bacteria belonging to the epsilon subdivision of Proteobacteria (epsilon Proteobacteria). Here, we report the first enrichments and characterizations of four epsilon Proteobacteria that are directly associated with Alvinella pompejana, a deep sea hydrothermal vent polychete, or with hydrothermal vent chimney samples. These novel bacteria were moderately thermophilic sulfur-reducing heterotrophs growing on formate as the energy and carbon source. In addition, two of them (Am-H and Ex-18.2) could grow on sulfur lithoautrotrophically using hydrogen as the electron donor. Optimal growth temperatures of the bacteria ranged from 41 to 45°C. Phylogenetic analysis of the small-subunit ribosomal gene of the two heterotrophic bacteria demonstrated 95% similarity to Sulfurospirillum arcachonense, an epsilon Proteobacteria isolated from an oxidized marine surface sediment. The autotrophic bacteria grouped within a deeply branching clade of the epsilon Proteobacteria, to date composed only of uncultured bacteria detected in a sample from a hydrothermal vent along the mid-Atlantic ridge. A molecular survey of various hydrothermal vent environments demonstrated the presence of two of these bacteria (Am-N and Am-H) in more than one geographic location and habitat. These results suggest that certain epsilon Proteobacteria likely fill important niches in the environmental habitats of deep-sea hydrothermal vents, where they contribute to overall carbon and sulfur cycling at moderate thermophilic temperatures.