Comparative analysis of midgut bacterial communities of Aedes aegypti mosquito strains varying in vector competence to dengue virus

Differences in midgut bacterial communities of Aedes aegypti, the primary mosquito vector of dengue viruses (DENV), might influence the susceptibility of these mosquitoes to infection by DENV. As a first step toward addressing this hypothesis, comparative analysis of bacterial communities from midguts of mosquito strains with differential genetic susceptibility to DENV was performed. 16S rRNA gene libraries and real-time PCR approaches were used to characterize midgut bacterial community composition and abundance in three Aedes aegypti strains: MOYO, MOYO-R, and MOYO-S. Although Pseudomonas spp.-related clones were predominant across all libraries, some interesting and potentially significant differences were found in midgut bacterial communities among the three strains. Pedobacter sp.- and Janthinobacterium sp.-related phylotypes were identified only in the MOYO-R strain libraries, while Bacillus sp. was detected only in the MOYO-S strain. Rahnella sp. was found in MOYO-R and MOYO strains libraries but was absent in MOYO-S libraries. Both 16S rRNA gene library and real-time PCR approaches confirmed the presence of Pedobacter sp. only in the MOYO-R strain. Further, real-time PCR-based quantification of 16S rRNA gene copies showed bacterial abundance in midguts of the MOYO-R strain mosquitoes to be at least 10–100-folds higher than in the MOYO-S and MOYO strain mosquitoes. Our study identified some putative bacteria with characteristic physiological properties that could affect the infectivity of dengue virus. This analysis represents the first report of comparisons of midgut bacterial communities with respect to refractoriness and susceptibility of Aedes aegypti mosquitoes to DENV and will guide future efforts to address the potential interactive role of midgut bacteria of Aedes aegypti mosquitoes in determining vectorial capacity for DENV.     

Antagonistic interactions between psychrotrophic cultivable bacteria isolated from Antarctic sponges: a preliminary analysis

The present work was aimed at studying antagonistic interactions existing among cultivable bacteria associated with the Antarctic sponges Anoxycalyx joubini and Lissodendoryx nobilis. Overall, bacterial isolates were affiliated with the α- and γ-Proteobacteria (17.3 and 65.3%, respectively), the CFB group of Bacteroidetes (10.7%) and the Actinobacteria (6.7%) by 16S rDNA sequencing. The two sponges harbored microorganisms belonging to different species/genera and previously retrieved from polar marine environments. Antagonistic interactions, assayed by the cross-streak method and statistically analyzed using the “network theory” approach, were checked among isolates associated with the same sponge as well as between isolates retrieved from the two sponge species (“cross-niche inhibition”). Results suggest that antagonism could play a significant role in shaping bacterial communities within sponge tissues. Data from this study confirm previous observations on the antibacterial activity of Antarctic microorganisms and represent a baseline for further investigation of both the ecological role and biotechnological exploitation of Antarctic sponge-associated bacteria.     

Vertical distribution of bacteria in a lake sediment from Antarctica by culture-independent and culture-dependent approaches

Bacterial diversity of the subsurface (18-22 cm), middle (60-64 cm) and bottom (100-104 cm) of a 136-cm-long sediment core sampled from a freshwater lake in Antarctica was determined by the culturable approach, T-RFLP and 16S rRNA gene clone libraries. Using the culturable approach, 41 strains were isolated and, based on phylogenetic analysis, they could be categorized into 14 groups. Representatives of the 14 groups varied in their growth temperature range (4-30 °C), in their tolerance to NaCl (0-2 M NaCl) and in the growth pH range (5-11). Eleven of fourteen representative strains exhibited either amylase, lipase, protease and (or) urease activities at 4 °C. Bacterial diversity at the phyla level using T-RFLP and 16S rRNA clone libraries was similar and clones were affiliated with Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. TRFs affiliated with Spirochaetes were detected only by the T-RFLP approach and clones affiliated with Caldiserica only in the clone libraries. Stratification of bacteria along the depth of the sediment was observed both with the T-RFLP and the 16S rRNA gene clone library methods, and results indicated that stratification was dependent on the nature of the organism, aerobic or anaerobic. For instance, aerobic Janthinobacterium and Polaromonas were confined to the surface of the sediment, whereas anaerobic Caldisericum was present only in the bottom portion of the core. It may be concluded that the bacterial diversity of an Antarctic lake sediment core sample varies throughout the length of the core depending on the oxic-anoxic conditions of the sediment. Furthermore, these psychrophilic bacteria, due to their ability to produce extracellular cold active enzymes, might play a key role in the transformation of complex organic compounds.     

Characterization of specificity of bacterial community structure within the burrow environment of the marine polychaete Hediste (Nereis) diversicolor

Bioturbation is known to stimulate microbial communities, especially in macrofaunal burrows where the abundance and activities of bacteria are increased. Until now, these microbial communities have been poorly characterized and an important ecological question remains: do burrow walls harbor similar or specific communities compared with anoxic and surface sediments? The bacterial community structure of coastal sediments inhabited by the polychaete worm Hediste diversicolor was investigated. Surface, burrow wall and anoxic sediments were collected at the Carteau beach (Gulf of Fos, Mediterranean Sea). Bacterial diversity was determined by analyzing small subunit ribosomal RNA (16S rRNA) sequences from three clone libraries (168, 179 and 129 sequences for the surface, burrow wall and anoxic sediments, respectively). Libraries revealed 306 different operational taxonomic units (OTUs) belonging to at least 15 bacterial phyla. Bioinformatic analyses and comparisons between the three clone libraries showed that the burrow walls harbored a specific bacterial community structure which differed from the surface and anoxic environments. More similarities were nevertheless found with the surface assemblage. Inside the burrow walls, the bacterial community was characterized by high biodiversity, which probably results from the biogeochemical heterogeneity of the burrow system.     

Microbial diversity at the moderate acidic stage in three different sulfidic mine tailings dumps generating acid mine drainage

In freshly deposited sulfidic mine tailings the pH is alkaline or circumneutral. Due to pyrite or pyrrhotite oxidation the pH is dropping over time to pH values <3 at which acidophilic iron- and sulfur-oxidizing prokaryotes prevail and accelerate the oxidation processes, well described for several mine waste sites. The microbial communities at the moderate acidic stage in mine tailings are only scarcely studied. Here we investigated the microbial diversity via 16S rRNA gene sequence analysis in eight samples (pH range 3.2–6.5) from three different sulfidic mine tailings dumps in Botswana, Germany and Sweden. In total 701 partial 16S rRNA gene sequences revealed a divergent microbial community between the three sites and at different tailings depths. Proteobacteria and Firmicutes were overall the most abundant phyla in the clone libraries. Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospira occurred less frequently. The found microbial communities were completely different to microbial communities in tailings at <pH 3 described in the literature.     

Phylogenetic diversity of bacterial communities in South China Sea mesoscale cyclonic eddy perturbations

Eddy pumping drives a set of biogeochemical processes by lifting deep waters into the euphotic zone. To address the potential effect of such physical processes upon the bacterial community, phylogenetic diversity was determined in two cold-core cyclonic eddies in the South China Sea. 16S rDNA terminal restriction fragment length polymorphism analysis of the microbial communities through the whole water column showed a wider depth range for the intermediate transition water mass at sites inside the eddies than for those outside. This water mass contained a relatively more complex community than the euphotic and deep-water zones. Stratification of prokaryotic populations between the surface and chlorophyll maximum layer of eddy-related sites versus homogeneity of communities in the euphotic zone of the reference site, revealed by statistical analysis of 16S rDNA libraries, is most likely a reflection of isopycnal displacement induced by differing water movement inside and outside eddies. Phylogenetic analysis revealed that eddy center sites were characterized by deep-water group Alteromonadales-affiliated clones, the psychrophilic genus Octadecabacter cluster and the nitrogen-fixing phototrophic Rhodospirillaceae cluster, while Paracoccus, an important functional group, abundantly existed at the reference site outside eddies. Our analysis revealed that bacterial community structure was significantly influenced by cyclonic eddy perturbations.     

Sequencing for complete rDNA sequences (18S, ITS1, 5.8S, ITS2, and 28S rDNA) of Demodex and phylogenetic analysis of Acari based on 18S and 28S rDNA

Due to the difficulty of DNA extraction for Demodex, few studies dealt with the identification and the phyletic evolution of Demodex at molecular level. In this study, we amplified, sequenced, and analyzed a complete (Demodex folliculorum) and an almost complete (D12 missing) (Demodex brevis) ribosomal DNA (rDNA) sequence and also analyzed the primary sequences of divergent domains in small-subunit ribosomal RNA (rRNA) of 51 species and in large-subunit rRNA of 43 species from four superfamilies in Acari (Cheyletoidea, Tetranychoidea, Analgoidea, and Ixodoidea). The results revealed that 18S rDNA sequence was relatively conserved in rDNA-coding regions and was not evolving as rapidly as 28S rDNA sequence. The evolutionary rates of transcribed spacer regions were much higher than those of the coding regions. The maximum parsimony trees of 18S and 28S rDNA appeared to be almost identical, consistent with their morphological classification. Based on the fact that the resolution capability of sequence length and the divergence of the 13 segments (D1–D6, D7a, D7b, and D8–D12) of 28S rDNA were stronger than that of the nine variable regions (V1–V9) of 18S rDNA, we were able to identify Demodex (Cheyletoidea) by the indels occurring in D2, D6, and D8.     

Endophytic bacterial diversity in roots of Typha angustifolia L. in the constructed Beijing Cuihu Wetland (China)

We investigated the community structure of endophytic bacteria in narrowleaf cattail (Typha angustifolia L.) roots growing in the Beijing Cuihu Wetland, China, using the 16S rDNA library technique. In total, 184 individual sequences were used to assess the diversity of endophytic bacteria. Phylogenetic analysis revealed that 161 clones (87.5%) were affiliated with Proteobacteria, other clones grouped into Cytophaga/Flexibacter/Bacteroids (3.3%), Fusobacteria (3.8%), and nearly 5% were uncultured bacteria. In Proteobacteria, the beta and gamma subgroups were the most abundant, accounting for approximately 46% and 36.6% of all Proteobacteria, respectively. The dominant genera included Rhodoferax, Pelomonas, Uliginosibacterium, Pseudomonas, Aeromonas, Rhizobium, Sulfurospirillum, Ilyobacter and Bacteroides. While some of these endophytic bacteria are capable of fixing nitrogen and can therefore improve plant growth, other endophytes may play important biological roles by removing nitrogen, phosphorus and/or organic matter from the water body and thus have the potential to enhance the phytoremediation of eutrophic water bodies. These bacteria have the potential to degrade xenobiota such as methane, methanol, methylated amines, catechol, oxochlorate, urea, cyanide, and 2,4-dichlorophenol. Hence, the use of certain endophytic bacteria in the process of phytoremediation could be a powerful approach for the restoration of eutrophic systems.     

Popular molecular markers in bacteria

Molecular markers are defined as the fragments of DNA sequence associated with a genome, which areused to identify a particular DNA sequence. Nowadays, with the explosive growth of genetic research and bacterial classification, molecular marker is an important tool to identify bacterial species. Taking account to its significant roles in clinic, medicine and food industry, in this review article, we summarize the traditional research and new development about molecular markers (also called genetic markers) in bacteria, including genes of 16S rRNA, 23S rRNA, rpoB, gyrB, dnaK, dsrAB, amoA, amoB, mip, horA, hitA, recA, ica, frc, oxc, 16S?C23S rDNA ISR and IS256.     

Change in gene abundance in the nitrogen biogeochemical cycle with temperature and nitrogen addition in Antarctic soils

The microbial community (bacterial, archaeal, and fungi) and eight genes involved in the nitrogen biogeochemical cycle (nifH, nitrogen fixation; bacterial and archaeal amoA, ammonia oxidation; narG, nitrate reduction; nirS, nirK, nitrite reduction; norB, nitric oxide reduction; and nosZ, nitrous oxide reduction) were quantitatively assessed in this study, via real-time PCR with DNA extracted from three Antarctic soils. Interestingly, AOB amoA was found to be more abundant than AOA amoA in Antarctic soils. The results of microcosm studies revealed that the fungal and archaeal communities were diminished in response to warming temperatures (10 °C) and that the archaeal community was less sensitive to nitrogen addition, which suggests that those two communities are well-adapted to colder temperatures. AOA amoA and norB genes were reduced with warming temperatures. The abundance of only the nifH and nirK genes increased with both warming and the addition of nitrogen. NirS-type denitrifying bacteria outnumbered NirK-type denitrifiers regardless of the treatment used. Interestingly, dramatic increases in both NirS and NirK-types denitrifiers were observed with nitrogen addition. NirK types increase with warming, but NirS-type denitrifiers tend to be less sensitive to warming. Our findings indicated that the Antarctic microbial nitrogen cycle could be dramatically altered by temperature and nitrogen, and that warming may be detrimental to the ammonia-oxidizing archaeal community. To the best of our knowledge, this is the first report to investigate genes associated with each process of the nitrogen biogeochemical cycle in an Antarctic terrestrial soil environment.     

Differentiation of Phylogenetically Related Slowly Growing Mycobacteria Based on 16S-23S rRNA Gene Internal Transcribed Spacer Sequences

Interspecific polymorphisms of the 16S rRNA gene (rDNA) are widely used for species identification of mycobacteria. 16S rDNA sequences, however, do not vary greatly within a species, and they are either indistinguishable in some species, for example, in Mycobacterium kansasii and M. gastri, or highly similar, for example, in M. malmoense and M. szulgai. We determined 16S-23S rDNA internal transcribed spacer (ITS) sequences of 60 strains in the genus Mycobacterium representing 13 species (M. avium, M. conspicuum, M. gastri, M. genavense, M. kansasii, M. malmoense, M. marinum, M. shimoidei, M. simiae, M. szulgai, M. triplex, M. ulcerans, and M. xenopi). An alignment of these sequences together with additional sequences available in the EMBL database (for M. intracellulare, M. phlei, M. smegmatis, and M. tuberculosis) was established according to primary- and secondary-structure similarities. Comparative sequence analysis applying different treeing methods grouped the strains into species-specific clusters with low sequence divergence between strains belonging to the same species (0 to 2%). The ITS-based tree topology only partially correlated to that based on 16S rDNA, but the main branching orders were preserved, notably, the division of fast-growing from slowly growing mycobacteria, separate branching for M. simiae, M. genavense, and M. triplex, and distinct branches for M. xenopi and M. shimoidei. Comparisons of M. gastri with M. kansasii and M. malmoense with M. szulgai revealed ITS sequence similarities of 93 and 88%, respectively. M. marinum and M. ulcerans possessed identical ITS sequences. Our results show that ITS sequencing represents a supplement to 16S rRNA gene sequences for the differentiation of closely related species. Slowly growing mycobacteria show a high sequence variation in the ITS; this variation has the potential to be used for the development of probes as a rapid approach to mycobacterial identification.     

Identification of Polybacterial Communities in Patients with Postoperative,Posttraumatic, and Endogenous Endophthalmitis through 16S rRNA Gene Libraries

Endophthalmitis is a potential vision-threatening complication following surgical procedures (postoperative endophthalmitis [POE]), trauma (posttraumatic endophthalmitis [PTE]), and bacteremic seeding of the eye from a distant infection site (endogenous endophthalmitis [EE]). Several studies have revealed the polybacterial characteristics of endophthalmitis, which make the administration of antibiotics to treat the disease challenging. However, until now, the polybacterial communities of POE, PTE, and EE have not been precisely studied. Hence, the present study was designed to identify the bacterial community of endophthalmitis through 16S rRNA gene libraries. Of the 40 intraocular samples tested, 30 libraries were constructed with bacterial nested-PCR-positive samples. The obtained recombinant clones were screened through amplified rRNA gene restriction analysis (ARDRA) to identify unique clones. The multiple types of ARDRA patterns (P = 0.345) and diverse bacterial sequences (P = 0.277) within the libraries revealed the polybacterial nature of infection in POE, PTE, and EE. Moreover, to the best of our knowledge, this is the first report on polybacterial infection in EE. Gram-positive bacteria, including Bacillus spp. (n = 19), Streptococcus spp. (n = 18), Staphylococcus spp. (n = 6), Exiguobacterium spp. (n = 3), Gemella spp. (n = 2), Enterococcus spp. (n = 2), a Lysinibacillus sp. (n = 1), a Clostridium sp. (n = 1), and a Nocardia sp. (n = 1), and Gram-negative bacteria, including Serratia spp. (n = 18), Pseudomonas spp. (n = 10), Enterobacter spp. (n = 8), Acinetobacter spp. (n = 3), Pantoea spp. (n = 3), a Haemophilus sp. (n = 1), and a Massilia sp. (n = 1), were identified. Interestingly, among them, 10 bacterial species were not previously reported to be associated with endophthalmitis or other ocular infections. Besides, the presence of 4 unidentifiable clones suggests the possibility of novel organisms that might cause eye infections. Therefore, it is recommended that, in addition to the polybacterial nature of POE, PTE, and EE infections, the spectrum of the pathogenic bacterial community identified in this work should be considered while administering antibiotic therapy in suspected endophthalmitis cases.     

Isolation and characterization of biocides resistant bacteria from dental unit water line biofilms

Six biocides resistant isolates were isolated from dental unit water lines (DUWL) in Pakistan. All isolates could tolerate 150 μg ml^–1 of biocides (5.25% sodium hypocholrite, 35% H₂O₂, 4% tween 20, 1% povidine iodine, 0.2% chlorohexidine gluconate, 1% ethylene di‐amino tetra acetic acid and 1% phenol) on l‐agar and 100 μg ml^–1 in l‐broth. The growth rate of all isolates was determined by generating growth curves at 37 °C for 48 h. The isolates were found to differ in growth rates with lag phase varying from (4–6 h) in biocides supplemented media compared to 2–4 h in biocides free medium. They have wide temperatures (24–42 °C) and pH (5–9) ranges. Traditional ways of identification of bacteria by phenotypic characteristics were accomplished by phenotypic and biochemical characterization. Heavy metals and antimicrobial susceptibility tests indicated that all isolates examined were resistant to trimethoprim, chloramphenicol while sensitive to HgCl₂ and Pb (NO₃)₂. Almost all isolates were opportunistic pathogens. The 16S rRNA‐encoding genes from these six isolates were sequenced to confirm the identity of these isolates. 5 different genera (Bacillus, Achromobacter, Pseudomonas and Klebsiella) of bacteria were identified by 16S rDNA genes amplified from genomic DNA of biocides resistant DUWL biofilm isolates. Analysis of 16S rDNA genes revealed a much more clear identification of microrganisms than culture methods. However, different species of the same genera can have the same 16S rRNA gene sequence but are different due to phenotypic differences or different clinical manifestations. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Complexity,Temporal Stability,and Clinical Correlates of Airway Bacterial Community Composition in Primary Ciliary Dyskinesia

Primary ciliary dyskinesia (PCD) is a genetic disease characterized by abnormalities in ciliary function, leading to compromised airway clearance and chronic bacterial infection of the upper and lower airways. The compositions of these infections and the relationships between their characteristics and disease presentation are poorly defined. We describe here the first systematic culture-independent evaluation of lower airway bacteriology in PCD. Thirty-three airway samples (26 from sputum, 7 from bronchoalveolar lavage [BAL] fluid) were collected from 24 PCD patients aged 4 to 73 years. 16S rRNA quantitative PCR and pyrosequencing were used to determine the bacterial loads and community compositions of the samples. Bacterial loads, which ranged from 1.3 × 10⁴ to 5.2 × 10⁹ CFU/ml, were positively correlated with age (P = 0.002) but not lung function. An analysis of ∼7,000 16S rRNA sequences per sample identified bacterial species belonging to 128 genera. The concurrently collected paired samples showed high bacterial community similarity. The mean relative abundance of the dominant genera was 64.5% (standard deviation [SD], 24.5), including taxa reported through standard diagnostic microbiology (members of the genera Pseudomonas, Haemophilus, and Streptococcus) and those requiring specific ex vivo growth conditions (members of the genera Prevotella and Porphyromonas). The significant correlations observed included a positive relationship between Pseudomonas aeruginosa relative abundance and age and a negative relationship between P. aeruginosa relative abundance and lung function. Members of the genus Ralstonia were also found to contribute substantially to the bacterial communities in a number of patients. Follow-up samples from a subset of patients revealed high levels of bacterial community temporal stability. The detailed microbiological characterization presented here provides a basis for the reassessment of the clinical management of PCD airway infections.     

Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis

Despite widespread use of antibiotics, few studies have measured their effects on the burden or diversity of bacteria in the mammalian intestine. We developed an oral antibiotic treatment protocol and characterized its effects on murine intestinal bacterial communities and immune cell homeostasis. Antibiotic administration resulted in a 10-fold reduction in the amount of intestinal bacteria present and sequencing of 16S rDNA segments revealed significant temporal and spatial effects on luminal and mucosal-associated communities including reductions in luminal Firmicutes and mucosal-associated Lactobacillus species, and persistence of bacteria belonging to the Bacteroidetes and Proteobacteria phyla. Concurrently, antibiotic administration resulted in reduced RELMβ production, and reduced production of interferon-γ and interleukin-17A by mucosal CD4⁺ T lymphocytes. This comprehensive temporal and spatial metagenomic analyses will provide a resource and framework to test the influence of bacterial communities in murine models of human disease.     

Genetic variability of anaplasmataceae bacteria determined in Haemaphysalis spp. and Dermacentor sp. Ticks on the territory of the Russian Far East

In total, 484 Haemaphysalis japonica, 359 Haemaphysalis concinna, and 221 Dermacentor silvarum collected in Amur oblast and Khabarovsk krai of the Russian Far East were examined regarding the presence of Anaplasmataceae bacteria using nested PCR. All positive samples were characterized by analysis of the 16S rRNA gene and/or groESL operone nucleotide sequences. Forty-nine H. japonica and three H. concinna were shown to contain DNA of two new Ehrlichia genetic variants. On the basis of 16S rRNA gene and groESL operone nucleotide sequences analysis, these genetic variants were found to be most closely related to Ehrlichia spp. revealed in Haemaphysalis spp. ticks in Japan. Four H. concinna from Amur oblast were shown to contain DNA of a new Anaplasma bovis genetic variant, which corresponded to the A. bovis genetic variant revealed in a red gray-backed vole and a Siberian chipmunk from the Far East. Three H. concinna and nine D. silvarum contained DNA of atypical bacteria that cannot be attributed to any Anaplasmataceae genera based on the determined sequences of the 16S rRNA gene fragments. The revealed atypical bacteria significantly differed from each other and did not form a separate genetic group on the basis of 16S rRNA gene sequences.     

Antarctic ice core samples: culturable bacterial diversity

Culturable bacterial abundance at 11 different depths of a 50.26 m ice core from the Tallaksenvarden Nunatak, Antarctica, varied from 0.02 to 5.8 × 10³ CFU ml^?1 of the melt water. A total of 138 bacterial strains were recovered from the 11 different depths of the ice core. Based on 16S rRNA gene sequence analyses, the 138 isolates could be categorized into 25 phylotypes belonging to phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. All isolates had 16S rRNA sequences similar to previously determined sequences (97.2–100%). No correlation was observed in the distribution of the isolates at the various depths either at the phylum, genus or species level. The 25 phylotypes varied in growth temperature range, tolerance to NaCl, growth pH range and ability to produce eight different extracellular enzymes at either 4 or 18 °C. Iso-, anteiso-, unsaturated and saturated fatty acids together constituted a significant proportion of the total fatty acid composition.     

Biodiversity of prokaryotic communities in sediments of different sub-basins of the Venice lagoon

Microbial community structure and diversity in the wide and shallow Venice lagoon were assessed, prior to construction of mobile dams, at nine stations representative of four different sub-basins previously selected on the basis of international guidelines for sediment quality. The sediments were mainly anoxic and were colonized by microbial communities the species richness of which was quantitatively correlated with total elemental sulfur and acid-volatile sulfide. Automated ribosomal intergenic spacer analysis clustered the stations into three groups. One station for each group was hence analyzed in detail for bacterial and archaeal diversity by screening of 16S rRNA gene clone libraries. The dominance of Gammaproteobacteria clones (84% with a high proportion of Vibrionaceae, indicator of urban pollution) determined significant divergence of the station adjacent to industrial and metropolitan areas. Bacteroidetes were widespread, especially where prairies of aquatic plants are located. The other two analyzed stations were dominated by bacterial taxa implicated in the sulfur cycle: the anoxygenic photosynthetic Chromatiales, sulfate- and sulfur-reducing Desulfobacterales and Desulfuromonadales, and members of the Alpha- and Epsilonproteobacteria.     

Structural differentiation of bacterial communities in indole-degrading bioreactors under denitrifying and sulfate-reducing conditions

The acclimated, anaerobic microbial community is an efficient method for indole-containing wastewater treatment. However, our understanding of the diversity of indole-degrading communities is still limited. We investigated two anaerobic, indole-decomposing microbial communities under both denitrifying and sulfate-reducing conditions. Utilizing a near full-length 16S rRNA gene clone library, the most dominant bacteria in the denitrifying bioreactor identified was β-proteobacteria. Among these, bacteria from genera Alicycliphilus, Acaligenes and Thauera were abundant and thought responsible for indole degradation. However, in the sulfate-reducing bioreactor, Clostridia and Actinobacteria were the dominant bacterial class found and likely the main degrading species. Microbial communities in these bioreactors shared only two operational taxonomic units (OTUs). Differences in the electron acceptors of denitrification or sulfate reduction may be responsible for the higher indole removal capacity in the denitrifying bioreactor (80%) than the capacity in the sulfate-reducing bioreactor (52%). This study is the first detailed analysis of an anaerobic indole-degrading community.