Reconstruction of ribosomal RNA genes from metagenomic data

Microbial indicators of efficient performance in an anaerobic/anoxic/aerobic integrated fixed-film activated sludge (A2O-IFAS) and a two-stage mesophilic anaerobic digestion process

An analysis of the community structure, diversity and population dynamics of Bacteria and Archaea in the suspended and attached biomass fractions of a pilot-scale anaerobic/anoxic/aerobic integrated fixed-film activated sludge (A²O-IFAS) was executed. Along with this, the effluents of the acidogenic (AcD) and methanogenic (MD) digesters of a two-stage mesophilic anaerobic (MAD) system treating the primary sludge (PS) and waste activated sludge (WAS) generated by the A²O-IFAS were also analyzed. Non-metric multidimensional scaling (MDS) and Biota-environment (BIO-ENV) multivariate analyses were performed to link population dynamics of Bacteria and Archaea to operating parameters and removal efficiencies of organic matter and nutrients, in search of microbial indicators associated with optimal performance. In all samples analyzed, Proteobacteria, Bacteroidetes and Chloroflexi were the most abundant phyla, while the hydrogenotrophic methanogens Methanolinea, Methanocorpusculum and Methanobacterium were the predominant archaeal genera. BIO-ENV analysis disclosed strong correlations between the population shifts observed in the suspended and attached bacterial communities of the A²O-IFAS and the removal rates of organic matter, N and P. It is noteworthy that the incorporation of carriers combined with a short sludge retention time (SRT = 4.0 ± 1.0 days) enhanced N removal performance of the A²O by favoring the enrichment of bacterial genera able to denitrify (Bosea, Dechloromonas, Devosia, Hyphomicrobium, Rhodobacter, Rhodoplanes, Rubrivivax, and Sulfuritalea) in the attached biomass fraction. In addition, operation at short SRT enabled the generation of a highly biodegradable WAS, which enhanced the biogas and methane yields in the two-stage MAD. An increase in the relative abundance of Acetobacteroides (uncultured Blvii28 wastewater-sludge group of Rikenellaceae family) correlated positively with the volatile solids removal rate (%VSR), CH₄ recovery rate and %CH₄ in the biogas (r > 0.8), supporting their relevance for an efficient methanogenesis in two-stage systems.

Genomic and Phenotypic Evaluation of Potential Probiotic Pediococcus Strains with Hypocholesterolemic Effect Isolated from Traditional Fermented Food

The use of probiotic microorganisms in food with the aim to confer health benefits to the host is one of the most critical roles of functional foods. Many pediococci bacteria frequently related to the meat environment, have technological properties, and are therefore commercially used as starter in the production of fermented meat products, such as different types of sausages. In this study, different lactic acid bacteria were isolated, identified to the species level, and then evaluated for their safety and functionality as possible probiotics. Different properties, such as resistance to simulated human gastrointestinal conditions, antimicrobial activity, and cholesterol-lowering effects, have been studied. Finally, the complete genome of one strain, namely P. acidilactici IRZ12B, which showed interesting features as a promising probiotic candidate, was sequenced and further studied. The results revealed that IRZ12B possesses interesting probiotic properties, particularly cholesterol-lowering capability and antimicrobial activity. In silico analysis evidenced the absence of plasmids, transmissible antibiotic resistance genes, and virulence factors. We also detected a bacteriocin encoding gene and a cholesterol assimilation-related protein. The phenotypical and genomic outcomes described in this study make P. acidilactici IRZ12B a very interesting cholesterol-lowering potential probiotic strain to be considered for the development of novel non-dairy-based functional foods.

Jellyfish swarm impair the pretreatment efficiency and membrane performance of seawater reverse osmosis desalination

Circumstantial evidence has suggested that jellyfish swarms impair the operation of seawater reverse osmosis desalination facilities. However, only limited information is currently available on the pretreatment efficiency of jellyfish and their effects on reverse osmosis (RO) membrane performance. Here, we have comprehensively tested the pretreatment efficiency of a dual-media gravity filter and cartridge micro-filtration following the addition of jellyfish into the feedwater. Concurrently, the fouling propensity and performance of the RO membranes were examined. We show that jellyfish demise resulted in seawater eutrophication that triggered a significant increase in bacterial biomass (∼50-fold), activity (∼7-fold), and release of transparent exopolymer particles (∼5-fold), peaking three days after the addition of jellyfish into the feedwater. In parallel, a significant reduction in permeate water flux was recorded (∼10%) while trans-membrane pressure sharply increased (15%), reaching the operation pressure limit of our system (75 bar) after five days. At the conclusion of the experiments, the membrane surface was heavily covered by large chunks of organic-rich material and multilayered biofilms. Our results provide a holistic view on the operational challenges of seawater reverse osmosis (SWRO) desalination triggered by jellyfish swarms in coastal areas. Following the above, it can be inferred that freshwater production will likely be halted three days after drawing the jellyfish into the pretreatment system. Outcomes from these results may lead to the development of science-based operational protocols to cope with growing occurrence of jellyfish swarms around the intake of SWRO desalination facilities worldwide.

Thermal resistance and high-performance microwave decontamination assessment of Bacillus endospores isolated from food-grade herbal extracts

Generally, endospore contamination can occur from different sources during product manufacturing in many industries and therefore lower its quality by affecting physicochemical properties and shelf-life. Bacterial endospores can germinate inside the product and produce several enzymes, which can cause several undesirable changes. This study assessed the spores thermal resistance and applied a microwave decontamination technique toward herbal extracts (Tilia tomentosa and Centella asiatica) containing ethanol or glycerol. Based on 16S rRNA analysis, the detected contaminant endospores belonged to different Bacillus species, namely B. subtilis, B. zhangzhouensis, and B. pumilus. The thermal resistance assessment using inoculated endospores in the actual products revealed B. pumilus T2 as the most resistant endospore to the heat treatments tested in both T. tomentosa and C. asiatica extracts. Finally, a high-performance microwave technique was used to decontaminate T. tomentosa extract against the mixture of Bacillus spores. Results from the microwave technique indicate that the increase of temperature from 100°C to 105°C not only decontaminated the product but also could dramatically decrease the effective thermal treatment time (10 times), which can benefit the product quality. The results provided in this study considerably contribute to improving an original decontamination method for products containing glycerol and ethanol with the most negligible effect on product quality.

MetaFunPrimer: an Environment-Specific, High-Throughput Primer Design Tool for Improved Quantification of Target Genes

Genes belonging to the same functional group may include numerous and variable gene sequences, making characterizing and quantifying difficult. Therefore, high-throughput design tools are needed to simultaneously create primers for improved quantification of target genes. We developed MetaFunPrimer, a bioinformatic pipeline, to design primers for numerous genes of interest. This tool also enables gene target prioritization based on ranking the presence of genes in user-defined references, such as environment-specific metagenomes. Given inputs of protein and nucleotide sequences for gene targets of interest and an accompanying set of reference metagenomes or genomes, MetaFunPrimer generates primers for ranked genes of interest. To demonstrate the usage and benefits of MetaFunPrimer, a total of 78 primer pairs were designed to target observed ammonia monooxygenase subunit A (amoA) genes of ammonia-oxidizing bacteria (AOB) in 1,550 publicly available soil metagenomes. We demonstrate computationally that these amoA-AOB primers can cover 94% of the amoA-AOB genes observed in the 1,550 soil metagenomes compared with a 49% estimated coverage by previously published primers. Finally, we verified the utility of these primer sets in incubation experiments that used long-term nitrogen fertilized or unfertilized soils. High-throughput quantitative PCR (qPCR) results and statistical analyses showed significant differences in relative quantification patterns between the two soils, and subsequent absolute quantifications also confirmed that target genes enumerated by six selected primer pairs were significantly more abundant in the nitrogen-fertilized soils. This new tool gives microbial ecologists a new approach to assess functional gene abundance and related microbial community dynamics quickly and affordably.

IMPORTANCE Amplification-based gene characterization allows for sensitive and specific quantification of functional genes. There is often a large diversity of genes represented for functional gene groups, and multiple primers may be necessary to target associated genes. Current primer design tools are limited to designing primers for only a few genes of interest. MetaFunPrimer allows for high-throughput primer design for various genes of interest and also allows for ranking gene targets by their presence and abundance in environmental data sets. Primers designed by this tool improve the characterization and quantification of functional genes in broad gene amplification platforms and can be powerful with high-throughput qPCR approaches.

Insights into the removal of pharmaceutically active compounds from sewage sludge by two-stage mesophilic anaerobic digestion

The removal efficiencies (REs) of twenty-seven pharmaceutically active compounds (PhACs) (eight analgesic/anti-inflammatories, six antibiotics, four β-blockers, two antihypertensives/diuretics, three lipid regulators and four psychiatric drugs) were evaluated in a pilot-scale two-stage mesophilic anaerobic digestion (MAD) system treating thickened sewage sludge from a pilot-scale A²O™ wastewater treatment plant (WWTP) which was fed with wastewater from the pre-treatment of the full-scale WWTP Murcia Este (Murcia, Spain). The MAD system was long-term operated using two different sets of sludge retention times (SRTs) for the acidogenic (AcD) and methanogenic (MD) digesters (phase I, 2 and 12 days; and phase II, 5 and 24 days, in AcD and MD, respectively). Quantitative PCR (qPCR) and Illumina MiSeq sequencing were used to estimate the absolute abundance of Bacteria, Archaea, and Fungi and investigate the structure, diversity and population dynamics of their communities in the AcD and MD effluents. The extension of the SRT from 12 (phase I) to 24 days (phase II) in the MD was significantly linked with an improved removal of carbamazepine, clarithromycin, codeine, gemfibrozil, ibuprofen, lorazepam, and propranolol. The absolute abundances of total Bacteria and Archaea were higher in the MD regardless of the phase, while the diversity of bacterial and archaeal communities was lower in phase II, in both digesters. Non-metric multidimensional scaling (MDS) plots showed strong negative correlations among phyla Proteobacteria and Firmicutes and between genera Methanosaeta and Methanosarcina throughout the full experimental period. Strong positive correlations were revealed between the relative abundances of Methanospirillum and Methanoculleus and the methanogenesis performance parameters (volatile solids removal, CH₄ recovery rate and %CH₄ in the biogas), which were also related to longer SRT. The REs of several PhACs (naproxen, ketoprofen, ofloxacin, fenofibrate, trimethoprim, and atenolol) correlated positively (r > 0.75) with the relative abundances of specific bacterial and archaeal groups, suggesting their participation in biodegradation/biotransformation pathways.

In depth metagenomic analysis in contrasting oil wells reveals syntrophic bacterial and archaeal associations for oil biodegradation in petroleum reservoirs

Microbial biodegradation of hydrocarbons in petroleum reservoirs has major consequences in the petroleum value and quality. The identification of microorganisms capable of in-situ degradation of hydrocarbons under the reservoir conditions is crucial to understand microbial roles in hydrocarbon transformation and the impact of oil exploration and production on energy resources. The aim of this study was to profile the metagenome of microbial communities in crude oils and associated formation water from two high temperature and relatively saline oil-production wells, where one has been subjected to water flooding (BA-2) and the other one is considered pristine (BA-1). The microbiome was studied in the fluids using shotgun metagenome sequencing. Distinct microbial compositions were revealed when comparing pristine and water flooded oil wells in contrast to the similar community structures observed between the aqueous and oil fluids from the same well (BA-2). The equal proportion of archaea and bacteria together with the greater anaerobic hydrocarbon degradation potential in the BA-1 pristine but degraded reservoir contrasted with the predominance of bacteria over archaea, aerobic pathways and lower frequency of anaerobic degradation genes in the BA-2 water flooded undegraded well. Our results suggest that Syntrophus, Syntrophomonas, candidatus Atribacteria and Synergistia, in association with mainly acetoclastic methanogenic archaea of the genus Methanothrix, were collectively responsible for the oil biodegradation observed in the pristine petroleum well BA-1. Conversely, the microbial composition of the water flooded oil well BA-2 was mainly dominated by the fast-growing and putatively aerobic opportunists Marinobacter and Marinobacterium. This presumable allochthonous community introduced a greater metabolic versatility, although oil biodegradation has not been detected hitherto perhaps due to in-reservoir unfavorable physicochemical conditions. These findings provide a better understanding of the petroleum reservoir microbiomes and their potential roles in biogeochemical processes occurring in environments with different geological and oil recovery histories.

Assessment of bacterial and fungal communities in a full-scale thermophilic sewage sludge composting pile under a semipermeable cover

Bacterial and fungal communities in a full-scale composting pile were investigated, with sewage sludge and a vegetal bulking agent as starting materials. Bacillales and Actinomycetales were predominant throughout the process, showing significant abundance. Ascomycota was the predominant fungal phylum during the thermophilic phase, with a shift to Basidiomycota at the end of the process. The bulking material was the principal contributor to both communities by the end of the process, with a signal above 50%. The presence of genera, such as Pedomicrobium, Ureibacillus and Tepidimicrobium at the end of the process, and Chaetomium and Arthrographis in the maturation phase, showed an inverse correlation with indicators of organic matter stabilisation. A semipermeable cover was an effective technology for excluding pathogens. These results indicate that changes in the microbial population and their interrelation with operational variables could represent a useful tool for monitoring composting processes.

Linking microbial diversity and population dynamics to the removal efficiency of pharmaceutically active compounds (PhACs) in an anaerobic/anoxic/aerobic (A2O) system

The removal efficiencies (REs) of nineteen pharmaceutically active compounds (PhACs) (six antibiotics-clarithromycin, ofloxacin, sulfadiazine, sulfamethazine, sulfamethoxazole and trimethoprim -, four β-blockers -atenolol, metoprolol, propranolol and sotalol-, two antihypertensives/diuretics -furosemide and hydrochlorothiazide-, three lipid regulators -bezafibrate, fenofibrate and gemfibrozil-, and four psychiatric medications -carbamazepine, diazepam, lorazepam and paroxetine) were ascertained in a pilot-scale anaerobic/anoxic/aerobic (A²O) system treating urban wastewater, long term operated during two experimental phases using different sets of environmental conditions and operating parameters. Illumina MiSeq sequencing was used to investigate the structure, diversity and population dynamics of bacteria, archaea and fungi communities in the activated sludge. The results showed that mixed liquor suspended solids (MLSS) and food-to-microorganisms ratio (F/M) were operational parameters significantly influencing the REs of five of the analyzed PhACs in the A²O system. Biota-environment (BIO-ENV) analysis revealed strong correlations between population shifts of the activated sludge community and the REs of PhACs of the different pharmaceutical families. Increased REs of clarithromycin, furosemide, bezafibrate and gemfibrozil were concomitant to higher relative abundances of bacterial phylotypes classified within the Rhodobacteraceae and Sphingomonadaceae (Alphaproteobacteria), while those of Betaproteobacteria, Chloroflexi and Methanomethylovorans (Euryarchaea) correlated positively with the REs of up to seven PhACs belonging to different therapeutic groups.

An examination of the microbial community and occurrence of potential human pathogens in rainwater harvested from different roofing materials

While harvested rainwater can serve as an alternative water supply, microbial contaminants within the collection system can negatively affect water quality. Here, we investigated the impact of roofing material on the microbial quality of rainwater freshly harvested from pilot-scale roofs (concrete tile, cool, green, Galvalume^® metal, and asphalt fiberglass shingle). The microbial quality of freshly harvested rainwater from six rain events over two years was analyzed by high-throughput sequencing and culture-dependent and -independent techniques. The concentrations of total coliform were significantly different among rainwaters harvested from the various roofing materials (p-value >0.05). However, the fecal coliform concentrations and the copy numbers of Enterococcus 23S rRNA genes and total Bacteria 16S rRNA genes did not vary by type of roofing material in a statistically significant way. Potential human pathogens such as Legionella, Escherichia coli O157:H7, Shiga-toxin-producing Escherichia coli, and adenovirus were detected at least once in rainwater harvested from the different roofing materials, even though the lowest occurrence of those potential human pathogens was noted from the metal roof. Also, substantial variation in the microbial communities from the different roofing materials was observed at the family and genus levels. These results demonstrate that the type of roofing material affects the microbial quality of freshly harvested rainwater, indicating that the choice of roofing material could shape the microbial community structure entering a rainwater storage tank. Given that detection of potential pathogens in the freshly harvested rainwater also differed between roofing materials, the type of roofing used to capture rainwater needs to be considered in rainwater harvesting system design, particularly if the water is intended for potable use.

Effect of live yeast Saccharomyces cerevisiae supplementation on the performance and cecum microbial profile of suckling piglets

One mechanism through which S. cerevisiae may improve the performance of pigs is by altering the composition of the gut microbiota, a response that may be enhanced by early postnatal supplementation of probiotics. To test this hypothesis, newborn piglets (16 piglets/group) were treated with either S. cerevisiae yeast (5 x 109 cfu/pig: Low) or (2.5 x 1010 cfu/piglet: High) or equivalent volume of sterile water (Control) by oral gavage every other day starting from day 1 of age until weaning (28±1 days of age). Piglet body weight was recorded on days 1, 3, 7, 10, 17, 24 and 28 and average daily gain (ADG) calculated for the total period. At weaning, piglets were euthanized to collect cecum content for microbial profiling by sequencing of the 16S rRNA gene. ADG was higher in both Low and High yeast groups than in Control group (P<0.05). Alpha diversity analyses indicated a more diverse microbiota in the Control group compared with Low yeast group; the High yeast being intermediate (P < 0.01). Similarly, Beta diversity analyses indicated differences among treatments (P = 0.03), mainly between Low yeast and Control groups (P = 0.02). The sparse Partial Least Squares Discriminant Analysis (sPLS-DA) indicated that Control group was discriminated by a higher abundance of Veillonella, Dorea, Oscillospira and Clostridium; Low yeast treated pigs by higher Blautia, Collinsella and Eubacterium; and High yeast treated pigs by higher Eubacterium, Anaerostipes, Parabacteroides, Mogibacterium and Phascolarctobacterium. Partial Least Squares (PLS) analysis showed that piglet ADG was positively correlated with genus Prevotella in High yeast group. Yeast supplementation significantly affected microbial diversity in cecal contents of suckling piglets associated with an improvement of short chain fatty acid producing bacteria in a dose-dependent manner. In conclusion, yeast treatment improved piglet performance and shaped the piglet cecum microbiota composition in a dose dependent way.

As release under the microbial sulfate reduction during redox oscillations in the upper Mekong delta aquifers, Vietnam: A mechanistic study

The impact of seasonal fluctuations linked to monsoon and irrigation generates redox oscillations in the subsurface, influencing the release of arsenic (As) in aquifers. Here, the biogeochemical control on As mobility was investigated in batch experiments using redox cycling bioreactors and As- and SO₄^2--amended sediment. Redox potential (E_h) oscillations between anoxic (-300-0 mV) and oxic condition (0-500 mV) were implemented by automatically modulating an admixture of N₂/CO₂ or compressed air. A carbon source (cellobiose, a monomer of cellulose) was added at the beginning of each reducing cycle to stimulate the metabolism of the native microbial community. Results show that successive redox cycles can decrease arsenic mobility by up to 92% during reducing conditions. Anoxic conditions drive mainly the conversion of soluble As(V) to As(III) in contrast to oxic conditions. Phylogenetic analyses of 16S rRNA amplified from the sediments revealed the presence of sulfate and iron - reducing bacteria, confirming that sulfate and iron reduction are key factors for As immobilization from the aqueous phase. As and S K-edge X-ray absorption spectroscopy suggested the association of Fe-(oxyhydr)oxides and the importance of pyrite (FeS_2(s)), rather than poorly ordered mackinawite (FeS_(s)), for As sequestration under oxidizing and reducing conditions, respectively. Finally, these findings suggest a role for elemental sulfur in mediating aqueous thioarsenates formation in As-contaminated groundwater of the Mekong delta.

Extant microbial communities in the partially desiccated Rincon de Parangueo maar crater lake in Mexico

Rincon de Parangueo is a maar where a perennial lake was present until the 1980s. A conspicuous feature of the lake’s sediments is the presence of bioherms and organo-sedimentary deposits produced by microbial communities. The gradual lake desiccation during the last 40 years has produced dramatic environmental changes inside the maar basin, which resulted in the formation of a highly saline-alkaline system with extant microorganisms. In this paper we succinctly describe the geologic setting where the microbial communities have developed inside of the maar crater and the results obtained from high-throughput sequencing methods to characterize the microbial component (Bacteria, Eukarya and Archaea) in endolithic mats of calcareous sediments, and microbial mats and free-living microorganisms in the soda ponds. The studied sites displayed different microbial communities with a diverse number of phylotypes belonging to Bacteria and Eukarya, contrasting with a much less diverse component in Archaea. The sequences here detected were related to environmental sequences from sites with extreme life conditions such as high alkalinity (alkaliphiles), high salinity (halophiles) and high temperature (thermophiles). Moreover, our results indicate an important unexplored endemic microbial biodiversity in the vestiges of the former lake that need to be studied.

Prospective observational case series evaluating middle ear fluid and tympanostomy tubes through pyrosequencing

OBJECTIVE

One of the most common sequelae of tympanostomy tube (TT) placement is post-tympanostomy tube otorrhea (PTTO). Granulation tissue formation has been reported in 5-13.8% of patients with TT placement. The purpose of this study is to determine the biodistribution of microorganisms on TTs and middle ear fluid obtained from patients with PTTO.

METHODS

This was a prospective observational study of subjects (6-months-16-years) who underwent standard of care treatment for chronic PTTO. Data was collected on diagnosis, existence of antibiotic resistance, duration of tube placement, and evidence of recurrent infection and/or PTTO. TTs and middle ear fluid were subjected to pyrosequencing; additionally, ear fluid samples were sent for culture-based laboratory diagnostics.

RESULTS

DNA-pyrosequencing analysis of bacteria from fluid and TTs of pediatric subjects with PTTO revealed a mixture of both aerobic and anaerobic populations. Retained tubes with minimal otorrhea revealed a predominance of Staphylococcus species, normal external auditory canal (EAC) microbiome, within middle ear fluid as well as on TTs. However, TTs with active mucopurulent otorrhea and granulation tissue unveiled prominence of Gram-negative facultative anaerobes such as Pseudomonas and Eikenella. Discrepancies in prominent bacteria were seen between standard culture-based techniques versus pyrosequencing.

CONCLUSION

Retained tympanostomy tubes are colonized primarily with normal flora of the EAC. However, mucopurulent otorrhea associated with granulation tissue formation revealed a prominence of Gram-negative facultative anaerobes. Standard culture-based diagnostics may identify bacteria, which are not predominant species of infection. Future studies are necessary to assess the association of Gram-negative facultative anaerobes with granulation tissue formation.

Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface

Optofluidic single-cell genome amplification was used to obtain genome sequences from sub-micron cells collected from the euphotic and mesopelagic zones of the northwestern Sargasso Sea. Plankton cells were visually selected and manually sorted with an optical trap, yielding 20 partial genome sequences representing seven bacterial phyla. Two organisms, E01-9C-26 (Gammaproteobacteria), represented by four single cell genomes, and Opi.OSU.00C, an uncharacterized Verrucomicrobia, were the first of their types retrieved by single cell genome sequencing and were studied in detail. Metagenomic data showed that E01-9C-26 is found throughout the dark ocean, while Opi.OSU.00C was observed to bloom transiently in the nutrient-depleted euphotic zone of the late spring and early summer. The E01-9C-26 genomes had an estimated size of 4.76-5.05 Mbps, and contained "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes. Metabolic reconstruction indicated E01-9C-26 are likely versatile methylotrophs capable of scavenging C1 compounds, methylated compounds, reduced sulfur compounds, and a wide range of amines, including D-amino acids. The genome sequences identified E01-9C-26 as a source of "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes, but are of unknown function. In contrast, Opi.OSU.00C genomes encode genes for catabolizing carbohydrate compounds normally associated with eukaryotic phytoplankton. This exploration of optofluidics showed that it was effective for retrieving diverse single-cell bacterioplankton genomes and has potential advantages in microbiology applications that require working with small sample volumes or targeting cells by their morphology.

Effect of semi-permeable cover system on the bacterial diversity during sewage sludge composting

Sewage sludge composting is a profitable process economically viable and environmentally friendly. In despite of there are several kind of composting types, the use of combined system of semipermeable cover film and aeration air-floor is widely developed at industrial scale. However, the knowledge of the linkages between microbial communities structure, enzyme activities and physico-chemical factors under these conditions it has been poorly explored. Thus, the aim of this study was to investigate the bacterial dynamic and community structure using next generation sequencing coupled to analyses of microbial enzymatic activity and culturable dependent techniques in a full-scale real composting plant. Sewage sludge composting process was conducted using a semi-permeable Gore-tex cover, in combination with an air-insufflation system. The highest values of enzymatic activities such as dehydrogenase, protease and arylsulphatase were detected in the first 5 days of composting; suggesting that during this period of time a greater degrading activity of organic matter took place. Culturable bacteria identified were in agreement with the bacteria found by massive sequencing technologies. The greatest bacterial diversity was detected between days 15 and 30, with Actinomycetales and Bacillales being the predominant orders at the beginning and end of the process. Bacillus was the most representative genus during all the process. A strong correlation between abiotic factors as total organic content and organic matter and enzymatic activities such as dehydrogenase, alkaline phosphatase, and ß-glucosidase activity was found. Bacterial diversity was strongly influenced by the stage of the process, community-structure change was concomitant with a temperature rise, rendering favorable conditions to stimulate microbial activity and facilitate the change in the microbial community linked to the degradation process. Moreover, results obtained confirmed that the use of semipermeable cover in the composting of sewage sludge allow a noticeable reduction in the process-time comparing to conventional open windrows.

Full-scale photobioreactor for biotreatment of olive washing water: Structure and diversity of the microalgae-bacteria consortium

The performance of a full-scale photobioreactor (PBR) for the treatment of olive washing water (OWW) was evaluated under different HRTs (5-2days). The system was able to treat up to 3926L OWWday^-1, and consisted of an activated-carbon pretreatment column and a tubular PBR unit (80 tubes, 98.17L volume, 2-m height, 0.25m diameter). PBR was an effective and environmentally friendly method for the removal of phenols, COD, BOD₅, turbidity and color from OWW (average efficiencies 94.84±0.55%, 85.86±1.24%, 99.12±0.17%, 95.86±0.98% and 87.24±0.91%, respectively). The diversity of total bacteria and microalgae in the PBR was analyzed using Illumina-sequencing, evaluating the efficiency of two DNA extraction methods. A stable microalgae-bacteria consortium was developed throughout the whole experimentation period, regardless of changes in HRT, temperature or solar radiation. MDS analyses revealed that the interplay between green algae (Sphaeropleales), cyanobacteria (Hapalosiphon) and Proteobacteria (Rhodopseudomonas, Azotobacter) played important roles in OWW bioremediation.

Planktonic Growth of Pseudomonas aeruginosa around a Dual-Species Biofilm Supports the Growth of Fusobacterium nucleatum within That Biofilm

PURPOSE

The goal of this study was to understand the potential interaction between Pseudomonas aeruginosa and Fusobacterium nucleatum within the middle ear.

METHODS

We examined the microbiota of ear fluid and tympanostomy tubes (TTs) obtained from patients with posttympanostomy tube otorrhea. We also examined biofilms formed by P. aeruginosa and F. nucleatum, singly or together, under aerobic or anaerobic conditions.

RESULTS

While the facultative anaerobe P. aeruginosa dominated the bacterial population within the ear fluid, strict anaerobes, including F. nucleatum, dominated bacterial populations within the TTs. F. nucleatum was able to grow under aerobic conditions only in the presence of P. aeruginosa, whose growth reduced the level of dissolved oxygen within the broth to nearly anoxic condition within 4 h after inoculation. The presence of P. aeruginosa allowed F. nucleatum to maintain its growth for 72 h within the dual-species biofilm but not within the planktonic growth. Visualization of the biofilms revealed coaggregation of P. aeruginosa and F. nucleatum.

CONCLUSION

Extrapolation of these results suggests that, within the middle ear fluid, the growth of P. aeruginosa produces the anaerobic conditions required for the growth of F. nucleatum, both within effusion and within biofilms.

Impact of food grade and nano-TiO2 particles on a human intestinal community

Titanium dioxide (TiO₂) nanoparticles (NPs) are used as an additive (E171 or INS171) in foods such as gum, candy and puddings. To address concerns about the potential hazardous effects of ingested NPs, the toxicity of these food-grade NPs was investigated with a defined model intestinal bacterial community. Each titania preparation (food-grade TiO₂ formulations, E171-1 and E171-6a) was tested at concentrations equivalent to those found in the human intestine after sampling 1-2 pieces of gum or candy (100-250 ppm). At the low concentrations used, neither the TiO₂ food additives nor control TiO₂ NPs had an impact on gas production and only a minor effect on fatty acids profiles (C16:00, C18:00, 15:1 w5c, 18:1 w9c and 18:1 w9c, p < 0.05). DNA profiles and phylogenetic distributions confirmed limited effects on the bacterial community, with a modest decrease in the relative abundance of the dominant Bacteroides ovatus in favor of Clostridium cocleatum (-13% and +14% respectively, p < 0.05). Such minor shifts in the treated consortia suggest that food grade and nano-TiO₂ particles do not have a major effect on human gut microbiota when tested in vitro at relevant low concentrations. However, the cumulative effects of chronic TiO₂ NP ingestion remain to be tested.

Impacts of chemical gradients on microbial community structure

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.

Process performance and bacterial community dynamics of partial-nitritation biofilters subjected to different concentrations of cysteine amino acid

Partial-nitritation processes are used for the biological treatment of high nitrogen-low organic carbon effluents, such as anaerobic digestion reject water. The release of certain products generated during the anaerobic digestion process, such as amino acids, could potentially reduce the performance of these partial-nitritation bioprocesses. To investigate this, four partial-nitritation biofilters were subjected to continuous addition of 0, 150, 300, and 500 mg L^-1 cysteine amino acid in their influents. The addition of the amino acid had an impact over the performance of the partial-nitritation process and the bacterial community dynamics of the systems analyzed. Ammonium oxidation efficiency decreased with the addition of the amino acid, and a net nitrogen elimination occurred in presence of cysteine through the operation period. Bacterial community dynamics showed a decrease of Nitrosomonas species and a proliferation of putative heterotrophs with nitrification capacity, such as Pseudomonas, or denitrification capacity, such as Denitrobacter or Alicycliphilus. The addition of cysteine irreversible affected the bioreactors, which could not achieve the performance obtained before the addition of the amino acid. A mathematical predictive equation of the process performance depending on cysteine concentration added and operational time under such concentration was developed. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1254-1263, 2016.

Microbial Diversity of Impact-Generated Habitats

Impact-generated lithologies have recently been identified as viable and important microbial habitats, especially within cold and arid regions such as the polar deserts on Earth. These unique habitats provide protection from environmental stressors, such as freeze-thaw events, desiccation, and UV radiation, and act to trap aerially deposited detritus within the fissures and pore spaces, providing necessary nutrients for endoliths. This study provides the first culture-independent analysis of the microbial community structure within impact-generated lithologies in a Mars analog environment, involving the analysis of 44,534 16S rRNA sequences from an assemblage of 21 rock samples that comprises three shock metamorphism categories. We find that species diversity increases (H = 2.4-4.6) with exposure to higher shock pressures, which leads to the development of three distinct populations. In each population, Actinobacteria were the most abundant (41%, 65%, and 59%), and the dominant phototrophic taxa came from the Chloroflexi. Calculated porosity (a function of shock metamorphism) for these samples correlates (R² = 0.62) with inverse Simpson indices, accounting for overlap in populations in the higher shock levels. The results of our study show that microbial diversity is tied to the amount of porosity in the target substrate (as a function of shock metamorphism), resulting in the formation of distinct microbial populations. Key Words: Microbial diversity-Endoliths-Impact melt-rocks-Mars-Astrobiology. Astrobiology 16, 775-786.

Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water

To decipher the influence of depth stratification and surface provincialism on the dark ocean prokaryotic community composition, we sampled the major deep-water masses in the eastern North Atlantic covering three biogeographic provinces. Their diversity was evaluated using ordination and canonical analysis of 454 pyrotag sequences. Variance partitioning suggested that 16% of the variation in the bacterial community composition was based on depth stratification while 9% of the variation was due to geographic location. General linear mixed effect models showed that the community of the subsurface waters was connected to the dark ocean prokaryotic communities in different biogeographic provinces. Cluster analysis indicated that some prokaryotic taxa are specific to distinct regions in bathypelagic water masses. Taken together, our data suggest that the dark ocean prokaryotic community composition of the eastern North Atlantic is primed by the formation and the horizontal transport of water masses.

Sample Processing Impacts the Viability and Cultivability of the Sponge Microbiome

Sponges host complex microbial communities of recognized ecological and biotechnological importance. Extensive cultivation efforts have been made to isolate sponge bacteria, but most still elude cultivation. To identify the bottlenecks of sponge bacterial cultivation, we combined high-throughput 16S rRNA gene sequencing with a variety of cultivation media and incubation conditions. We aimed to determine the extent to which sample processing and cultivation conditions can impact bacterial viability and recovery in culture. We isolated 325 sponge bacteria from six specimens of Cymbastela concentrica and three specimens of Scopalina sp. These isolates were distributed over 37 different genera and 47 operational taxonomic units (defined at 97% 16S rRNA gene sequence identity). The cultivable bacterial community was highly specific to its sponge host and different media compositions yielded distinct microbial isolates. Around 97% of the isolates could be detected in the original sponge and represented a large but highly variable proportion (0.5–92% total abundance, depending on sponge species) of viable bacteria obtained after sample processing, as determined by propidium monoazide selective DNA modification of compromised cells. Our results show that the most abundant viable bacteria are also the most predominant groups found in cultivation, reflecting, to some extent, the relative abundances of the viable bacterial community, rather than the overall community estimated by direct molecular approaches. Cultivation is therefore shaped not only by the growth conditions provided, but also by the different cell viabilities of the bacteria that constitute the cultivation inoculum. These observations highlight the need to perform experiments to assess each method of sample processing for its accurate representation of the actual in situ bacterial community and its yield of viable cells.

Impact of methionine on a partial-nitritation biofilter

It has been demonstrated that an anaerobic digestion process cannot attain an efficient removal of several amino acids, with methionine being one of the most persistent of these. Thus, the effect that methionine amino acid has over the partial-nitritation process with fixed-biofilm configuration in terms of performance and bacterial community dynamics has been investigated. With respect to the performance with no addition, 100 mg/L methionine loading decreased ammonium oxidation efficiency in 60% and 100% at concentrations of 300 and 500 mg/L methionine, respectively. Bacterial biomass sharply increased by 30, 65, and 230% with the addition of 100, 300, and 500 mg/L methionine, respectively. Bacterial community analysis showed that methionine addition supported the proliferation of a diversity of heterotrophic genera, such as Lysobacter and Micavibrio, and reduced the relative abundance of ammonium oxidizing genus Nitrosomonas. This research shows that the addition of methionine affects the performance of the partial-nitritation process. In this sense, amino acids can pose a threat for the of partial-nitritation process treating anaerobic digester supernatant at full-scale implementation.

Comparison of bacterial communities of conventional and A-stage activated sludge systems

The bacterial community structure of 10 different wastewater treatment systems and their influents has been investigated through pyrosequencing, yielding a total of 283486 reads. These bioreactors had different technological configurations: conventional activated sludge (CAS) systems and very highly loaded A-stage systems. A-stage processes are proposed as the first step in an energy producing municipal wastewater treatment process. Pyrosequencing analysis indicated that bacterial community structure of all influents was similar. Also the bacterial community of all CAS bioreactors was similar. Bacterial community structure of A-stage bioreactors showed a more case-specific pattern. A core of genera was consistently found for all influents, all CAS bioreactors and all A-stage bioreactors, respectively, showing that different geographical locations in The Netherlands and Spain did not affect the functional bacterial communities in these technologies. The ecological roles of these bacteria were discussed. Influents and A-stage bioreactors shared several core genera, while none of these were shared with CAS bioreactors communities. This difference is thought to reside in the different operational conditions of the two technologies. This study shows that bacterial community structure of CAS and A-stage bioreactors are mostly driven by solids retention time (SRT) and hydraulic retention time (HRT), as suggested by multivariate redundancy analysis.

Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads

BACKGROUND

Anaerobic digestion is a biological process in which a consortium of microorganisms transforms a complex substrate into methane and carbon dioxide. A good understanding of the interactions between the populations that form this consortium can contribute to a successful anaerobic digestion of the substrate. In this study we combine the analysis of the biogas production in a laboratory anaerobic digester fed with the microalgae Spirulina, a protein rich substrate, with the analysis of the metagenome of the consortium responsible for digestion, obtained by high-throughput DNA sequencing. The obtained metagenome was also compared with a metagenome from a full scale biogas plant fed with cellulose rich material.

RESULTS

The optimal organic loading rate for the anaerobic digestion of Spirulina was determined to be 4.0 g Spirulina L(-1) day(-1) with a specific biogas production of 350 mL biogas g Spirulina (-1) with a methane content of 68 %. Firmicutes dominated the microbial consortium at 38 % abundance followed by Bacteroidetes, Chloroflexi and Thermotogae. Euryarchaeota represented 3.5 % of the total abundance. The most abundant organism (14.9 %) was related to Tissierella, a bacterium known to use proteinaceous substrates for growth. Methanomicrobiales and Methanosarcinales dominated the archaeal community. Compared to the full scale cellulose-fed digesters, Pfam domains related to protein degradation were more frequently detected and Pfam domains related to cellulose degradation were less frequent in our sample.

CONCLUSIONS

The results presented in this study suggest that Spirulina is a suitable substrate for the production of biogas. The proteinaceous substrate appeared to have a selective impact on the bacterial community that performed anaerobic digestion. A direct influence of the substrate on the selection of specific methanogenic populations was not observed.

Obtaining long 16S rDNA sequences using multiple primers and its application on dioxin-containing samples

Background

Next-generation sequencing (NGS) technology has transformed metagenomics because the high-throughput data allow an in-depth exploration of a complex microbial community. However, accurate species identification with NGS data is challenging because NGS sequences are relatively short. Assembling 16S rDNA segments into longer sequences has been proposed for improving species identification. Current approaches, however, either suffer from amplification bias due to one single primer or insufficient 16S rDNA reads in whole genome sequencing data.

Results

Multiple primers were used to amplify different 16S rDNA segments for 454 sequencing, followed by 454 read classification and assembly. This permitted targeted sequencing while reducing primer bias. For test samples containing four known bacteria, accurate and near full-length 16S rDNAs of three known bacteria were obtained. For real soil and sediment samples containing dioxins in various concentrations, 16S rDNA sequences were lengthened by 50% for about half of the non-rare microbes, and 16S rDNAs of several microbes reached more than 1000 bp. In addition, reduced primer bias using multiple primers was illustrated.

Conclusions

A new experimental and computational pipeline for obtaining long 16S rDNA sequences was proposed. The capability of the pipeline was validated on test samples and illustrated on real samples. For dioxin-containing samples, the pipeline revealed several microbes suitable for future studies of dioxin chemistry.

Reconstructing 16S rRNA genes in metagenomic data

Metagenomic data, which contains sequenced DNA reads of uncultured microbial species from environmental samples, provide a unique opportunity to thoroughly analyze microbial species that have never been identified before. Reconstructing 16S ribosomal RNA, a phylogenetic marker gene, is usually required to analyze the composition of the metagenomic data. However, massive volume of dataset, high sequence similarity between related species, skewed microbial abundance and lack of reference genes make 16S rRNA reconstruction difficult. Generic de novo assembly tools are not optimized for assembling 16S rRNA genes. In this work, we introduce a targeted rRNA assembly tool, REAGO (REconstruct 16S ribosomal RNA Genes from metagenOmic data). It addresses the above challenges by combining secondary structure-aware homology search, zproperties of rRNA genes and de novo assembly. Our experimental results show that our tool can correctly recover more rRNA genes than several popular generic metagenomic assembly tools and specially designed rRNA construction tools.

AVAILABILITY AND IMPLEMENTATION

The source code of REAGO is freely available at https://github.com/chengyuan/reago.

Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome

A haloalkaline anaerobic microbial community obtained from soda lake sediments was used to inoculate anaerobic reactors for the production of methane rich biogas. The microalga Spirulina was successfully digested by the haloalkaline microbial consortium at alkaline conditions (pH 10, 2.0 M Na(+)). Continuous biogas production was observed and the obtained biogas was rich in methane, up to 96%. Alkaline medium acted as a CO2 scrubber which resulted in low amounts of CO2 and no traces of H2S in the produced biogas. A hydraulic retention time (HRT) of 15 days and 0.25 g Spirulina L(-1) day(-1) organic loading rate (OLR) were identified as the optimal operational parameters. Metagenomic and metatranscriptomic analysis showed that the hydrolysis of the supplied substrate was mainly carried out by Bacteroidetes of the "ML635J-40 aquatic group" while the hydrogenotrophic pathway was the main producer of methane in a methanogenic community dominated by Methanocalculus.

Bacterial diversity of Drass, cold desert in Western Himalaya, and its comparison with Antarctic and Arctic

Drass is the coldest inhabited place in India and the second coldest, inhabited place in the world, after Siberia. Using the 16SrDNA amplicon pyrosequencing, bacterial diversity patterns were cataloged across the Drass cold desert. In order to identify the ecotype abundance across cold desert environment, bacterial diversity patterns of Drass were further compared with the bacterial diversity of two other cold deserts, i.e., Antarctic and Arctic. Acidobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Gemmatimonadetes were among the highly abundant taxonomic groups present across all the three cold deserts and were designated as the core phyla. However, Firmicutes, Nitrospirae, Armatimonadetes (former candidate division OP10), Planctomycetes, TM7, Chloroflexi, Deinococcus-Thermus, Tenericutes and candidate phyla WS3 were identified as rare phyla in Drass, Antarctic and Arctic samples. Differential abundance patterns were also computed across all the three samples, i.e., Acidobacteria (32.1 %) were dominant in Drass and Firmicutes (52.9 ± 17.6 %) and Proteobacteria (42 ± 1.3 %) were dominant in Antarctic and Arctic reference samples, respectively. Alpha diversity values Shannon's (H) and Simpson's (1-D) diversity indices were highest for Antarctic samples, whereas richness estimators (ACE and Chao1) were maximum for Drass soil suggesting greater species richness in bacterial communities in Drass than the Antarctic and Arctic samples.

METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

The ribosomal rRNA genes are widely used as genetic markers for taxonomic identification of microbes. Particularly the small subunit (SSU; 16S/18S) rRNA gene is frequently used for species- or genus-level identification, but also the large subunit (LSU; 23S/28S) rRNA gene is employed in taxonomic assignment. The METAXA software tool is a popular utility for extracting partial rRNA sequences from large sequencing data sets and assigning them to an archaeal, bacterial, nuclear eukaryote, mitochondrial or chloroplast origin. This study describes a comprehensive update to METAXA - METAXA2 - that extends the capabilities of the tool, introducing support for the LSU rRNA gene, a greatly improved classifier allowing classification down to genus or species level, as well as enhanced support for short-read (100 bp) and paired-end sequences, among other changes. The performance of METAXA2 was compared to other commonly used taxonomic classifiers, showing that METAXA2 often outperforms previous methods in terms of making correct predictions while maintaining a low misclassification rate. METAXA2 is freely available from http://microbiology.se/software/metaxa2/.

Deciphering metatranscriptomic data

Metatranscriptomic data contributes another piece of the puzzle to understanding the phylogenetic structure and function of a community of organisms. High-quality total RNA is a bountiful mixture of ribosomal, transfer, messenger and other noncoding RNAs, where each family of RNA is vital to answering questions concerning the hidden microbial world. Software tools designed for deciphering metatranscriptomic data fall under two main categories: the first is to reassemble millions of short nucleotide fragments produced by high-throughput sequencing technologies into the original full-length transcriptomes for all organisms within a sample, and the second is to taxonomically classify the organisms and determine their individual functional roles within a community. Species identification is mainly established using the ribosomal RNA genes, whereas the behavior and functionality of a community is revealed by the messenger RNA of the expressed genes. Numerous chemical and computational methods exist to separate families of RNA prior to conducting further downstream analyses, primarily suitable for isolating mRNA or rRNA from a total RNA sample. In this chapter, we demonstrate a computational technique for filtering rRNA from total RNA using the software SortMeRNA. Additionally, we propose a post-processing pipeline using the latest software tools to conduct further studies on the filtered data, including the reconstruction of mRNA transcripts for functional analyses and phylogenetic classification of a community using the ribosomal RNA.

Isolation and metagenomic characterization of bacteria associated with calcium carbonate and struvite precipitation in a pure moving bed biofilm reactor-membrane bioreactor

A bench-scale pure moving bed bioreactor-membrane bioreactor (MBBR-MBR) used for the treatment of urban wastewater was analyzed for the identification of bacterial strains with the potential capacity for calcium carbonate and struvite biomineral formation. Isolation of mineral-forming strains on calcium carbonate and struvite media revealed six major colonies with a carbonate or struvite precipitation capacity in the biofouling on the membrane surface and showed that heterotrophic bacteria with the ability to precipitate calcium carbonate and struvite constituted ~7.5% of the total platable bacteria. These belonged to the genera Lysinibacillus, Trichococcus, Comamomas and Bacillus. Pyrosequencing analysis of the microbial communities in the suspended cells and membrane biofouling showed a high degree of similarity in all the samples collected with respect to bacterial assemblage. The study of operational taxonomic units (OTUs) identified through pyrosequencing suggested that ~21% of the total bacterial community identified in the biofouling could potentially form calcium carbonate or struvite crystals in the pure MBBR-MBR system used for the treatment of urban wastewater.

Effect of ciprofloxacin antibiotic on the partial-nitritation process and bacterial community structure of a submerged biofilter

A partial-nitritation bench-scale submerged biofilter was used for the treatment of synthetic wastewater containing a high concentration of ammonium in order to study the influence of the antibiotic ciprofloxacin on the partial-nitritation process and biodiversity of the bacterial community structure. The influence of ciprofloxacin was evaluated in four partial-nitritation bioreactors working in parallel, which received sterile synthetic wastewater amended with 350 ng/L of ciprofloxacin (Experiment 1), synthetic wastewater without ciprofloxacin (Experiment 2), synthetic wastewater amended with 100 ng/L of ciprofloxacin (Experiment 3) and synthetic wastewater amended with 350 ng/L of ciprofloxacin (Experiment 4). The concentration of 100 ng/L of antibiotics demonstrated that the partial-nitritation process, microbial biomass and bacterial structure generated by tag-pyrosequencing adapted progressively to the conditions in the bioreactor. However, high concentrations of ciprofloxacin (350 ng/L) induced a decay of the partial-nitritation process, while the total microbial biomass was increased. Within the same experiment, the bacterial community experienced sequential shifts with a clear reduction of the ammonium oxidation bacteria (AOB) and an evident increase of Commamonas sp., which have been previously reported to be ciprofloxacin-resistant. Our study suggests the need for careful monitoring of the concentration of antibiotics such as ciprofloxacin in partial-nitritation bioreactors, in order to choose and maintain the most appropriate conditions for the proper operation of the system.

High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions

The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. Although the high-throughput nature of such methods enables the detection of low-frequency bacteria, these advances come at the cost of sequencing read length, limiting the phylogenetic resolution possible by current methods. Here, we present a generic approach for integrating short reads from large genomic regions, thus enabling phylogenetic resolution far exceeding current methods. The approach is based on a mapping to a statistical model that is later solved as a constrained optimization problem. We demonstrate the utility of this method by analyzing human saliva and Drosophila samples, using Illumina single-end sequencing of a 750 bp amplicon of the 16S rRNA gene. Phylogenetic resolution is significantly extended while reducing the number of falsely detected bacteria, as compared with standard single-region Roche 454 Pyrosequencing. Our approach can be seamlessly applied to simultaneous sequencing of multiple genes providing a higher resolution view of the composition and activity of complex microbial communities.

RNA-CODE: a noncoding RNA classification tool for short reads in NGS data lacking reference genomes

The number of transcriptomic sequencing projects of various non-model organisms is still accumulating rapidly. As non-coding RNAs (ncRNAs) are highly abundant in living organism and play important roles in many biological processes, identifying fragmentary members of ncRNAs in small RNA-seq data is an important step in post-NGS analysis. However, the state-of-the-art ncRNA search tools are not optimized for next-generation sequencing (NGS) data, especially for very short reads. In this work, we propose and implement a comprehensive ncRNA classification tool (RNA-CODE) for very short reads. RNA-CODE is specifically designed for ncRNA identification in NGS data that lack quality reference genomes. Given a set of short reads, our tool classifies the reads into different types of ncRNA families. The classification results can be used to quantify the expression levels of different types of ncRNAs in RNA-seq data and ncRNA composition profiles in metagenomic data, respectively. The experimental results of applying RNA-CODE to RNA-seq of Arabidopsis and a metagenomic data set sampled from human guts demonstrate that RNA-CODE competes favorably in both sensitivity and specificity with other tools. The source codes of RNA-CODE can be downloaded at http://www.cse.msu.edu/~chengy/RNA_CODE.

Marine microbial symbiosis heats up: the phylogenetic and functional response of a sponge holobiont to thermal stress

Large-scale mortality of marine invertebrates is a major global concern for ocean ecosystems and many sessile, reef-building animals, such as sponges and corals, are experiencing significant declines through temperature-induced disease and bleaching. The health and survival of marine invertebrates is often dependent on intimate symbiotic associations with complex microbial communities, yet we have a very limited understanding of the detailed biology and ecology of both the host and the symbiont community in response to environmental stressors, such as elevated seawater temperatures. Here, we use the ecologically important sponge Rhopaloeides odorabile as a model to explore the changes in symbiosis during the development of temperature-induced necrosis. Expression profiling of the sponge host was examined in conjunction with the phylogenetic and functional structure and the expression profile of the symbiont community. Elevated temperature causes an immediate stress response in both the host and symbiont community, including reduced expression of functions that mediate their partnership. Disruption to nutritional interdependence and molecular interactions during early heat stress further destabilizes the holobiont, ultimately leading to the loss of archetypal sponge symbionts and the introduction of new microorganisms that have functional and expression profiles consistent with a scavenging lifestyle, a lack virulence functions and a high growth rate. Previous models have postulated various mechanisms of mortality and disease in marine invertebrates. Our study suggests that interruption of symbiotic interactions is a major determinant for mortality in marine sessile invertebrates. High symbiont specialization and low functional redundancy, thus make these holobionts extremely vulnerable to environmental perturbations, including climate change.

Assembling full-length rRNA genes from short-read metagenomic sequence datasets using EMIRGE

Microbial ecologists have reaped enormous benefit from advances in high-throughput DNA sequencing. However, the short read lengths of currently dominant technologies have made a seemingly simple question about shotgun metagenomic experiments difficult to answer: what small subunit ribosomal RNA (SSU rRNA) genes are present in a sequenced biological sample? Without these gene sequences, it is difficult to interpret a sample within the rich context of ribosomal rRNA databases accumulated over decades. This chapter presents specialized software, EMIRGE, for the assembly of SSU rRNA genes. EMIRGE is optimized to deal with strain similarity and the fluctuating levels of conservation within the SSU rRNA gene that make assembly difficult. It has been used to successfully assemble genes from shotgun metagenomes, long PCR amplicons, and total-RNA transcriptomes. A detailed discussion of how EMIRGE works and how it deals with the uncertainty inherent in the assembly problem is presented. Practical suggestions are given for understanding and optimizing parameter choice, data preprocessing and postprocessing, and creation of a candidate SSU rRNA gene database. When high-throughput sequencing data are available, EMIRGE can serve as a valuable tool for interpreting microbial community structure.

Structural and functional insights from the metagenome of an acidic hot spring microbial planktonic community in the Colombian Andes

A taxonomic and annotated functional description of microbial life was deduced from 53 Mb of metagenomic sequence retrieved from a planktonic fraction of the Neotropical high Andean (3,973 meters above sea level) acidic hot spring El Coquito (EC). A classification of unassembled metagenomic reads using different databases showed a high proportion of Gammaproteobacteria and Alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16S rRNA gene fragments we observed the presence of Proteobacteria, micro-algae chloroplast and Firmicutes. Reads mapped against the genomes Acidiphilium cryptum JF-5, Legionella pneumophila str. Corby and Acidithiobacillus caldus revealed the presence of transposase-like sequences, potentially involved in horizontal gene transfer. Functional annotation and hierarchical comparison with different datasets obtained by pyrosequencing in different ecosystems showed that the microbial community also contained extensive DNA repair systems, possibly to cope with ultraviolet radiation at such high altitudes. Analysis of genes involved in the nitrogen cycle indicated the presence of dissimilatory nitrate reduction to N2 (narGHI, nirS, norBCDQ and nosZ), associated with Proteobacteria-like sequences. Genes involved in the sulfur cycle (cysDN, cysNC and aprA) indicated adenylsulfate and sulfite production that were affiliated to several bacterial species. In summary, metagenomic sequence data provided insight regarding the structure and possible functions of this hot spring microbial community, describing some groups potentially involved in the nitrogen and sulfur cycling in this environment.