Molecular evidence for novel planctomycete diversity in a municipal wastewater treatment plant

Deciphering Indigenous Bacterial Diversity of Co-Polluted Sites to Unravel Its Bioremediation Potential: A Metagenomic Approach

Polluted drains across the globe are affected due to reckless disposal of untreated industrial effluents resulting in significant water pollution affecting microbial community structure/dynamics. To elucidate this, polluted samples were collected from Budha Nala (BN) drain, Tung Dhab (TD) drain, and wastewater treatment plant (WWTP) receiving an inflow of organic pollutants as well as heavy metals due to anthropogenic activities. The sample of unpolluted pristine soil (PS) was used as control, as there is no history of usage of organic chemicals at this site. The bacterial diversity of these samples was sequenced using the Illumina MiSeq platform by amplifying the V3/V4 region of 16S rRNA. The majority of operational taxonomic unit (OTUs) at polluted sites belonged to phyla Proteobacteria specifically Gammaproteobacteria class, followed by Actinobacteria, Bacteriodetes, Chloroflexi, Firmicutes, Planctomycetes, WS6, and TM7, whereas unpolluted site revealed the prevalence of Proteobacteria followed by Actinobacteria, Planctomycetes, Firmicutes, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, and Nitrospirae. The data sets decode unclassified species of the phyla Proteobacteria, Bacteriodetes, Chloroflexi, Firmicutes, and WS6, along with some unclassified bacterial species. The study provided a comparative study of changed microbial community structure, their possible functions across diverse geographical locations, and identifying specific bacterial genera as pollution bio-indicators of aged polluted drains.

Distinct microbial communities enriched in water-saturated and unsaturated reactors influence performance of integrated hydroponics-microbial electrochemical technology

This study aimed to understand the wastewater treatment and electricity generation performance besides the microbial communities of the integrated Hydroponics-Microbial Electrochemical Technology (iHydroMET) systems operated with water-saturated and water-unsaturated reactors. The organics removal was slightly higher in the water-unsaturated system (93 ± 4 %) than in the water-saturated system (87 ± 2 %). The total nitrogen removal and electric voltage were considerably higher in the water-saturated system (42 ± 5 %; 111 ± 8 V per reactor) than in the water-unsaturated system (18 ± 3 %; 95 ± 9 V per reactor). The enhanced organics and nitrogen removal and high voltage output in respective conditions were due to the dominance of polysaccharide-degrading aerobes (e.g., Pirellula), anammox bacteria (e.g., Anammoximicrobium), denitrifiers (e.g., Thauera and Rheinheimera), and electroactive microorganisms (e.g., Geobacter). The differential performance governed by distinct microbial communities under the tested conditions indicates that an appropriate balancing of water saturation and unsaturation in reactors is crucial to achieving optimum iHydroMET performance.

The influence of the phylum Planctomycetota in the environmental resistome

Antimicrobial resistance is one of the leading causes of death worldwide and research on this topic has been on the spotlight for a long time. More recently and in agreement with the One Health Approach, the focus has moved towards the environmental resistome. Members of the phylum Planctomycetota are ubiquitously present in the environment including in hotspots for antimicrobial resistance selection and dissemination. Furthermore, phenotypic broad-range resistance has been observed in diverse members of this phylum. Here we review the evidence available on antimicrobial resistance in the underexploited Planctomycetota and highlight key aspects for future studies.

Pretreatment of marine sediment for the removal of di-(2-ethylhexyl) phthalate by sulfite in the presence of sorghum distillery residue-derived biochar and its effect on microbiota response

This study investigates the mechanism behind the oxidation di-(2-ethylhexyl) phthalate (DEHP) in marine sediment by coupling sulfite using biochar prepared from sorghum distillery residue (SDRBC). The rationale for this investigation stems from the need to seek effective methods for DEHP-laden marine sediment remediation. The aim is to assess the feasibility of sulfite-based advanced oxidation processes for treating hazardous materials such as DEHP containing sediment. To this end, the sediment in question was treated with 2.5 × 10-5 M of sulfite and 1.7 g L-1 of SDRBC700 at acidic pH. Additionally, the study demonstrated that the combination of SDRBC/sulfite with a bacterial system enhances DEHP removal. Thermostilla bacteria were enriched, highlighting their role in sediment treatment. This study concludes that sulfite-associated sulfate radicals-driven carbon advanced oxidation process (SR-CAOP) offers sustainable sediment pretreatment through the SDRBC/sulfite-mediated microbial consortium, in which the SO3•- and 1O2 were responsible for DEHP degradation. SDRBC/sulfite offers an effective and environmentally friendly method for removing DEHP. Further, these results can be targeted at addressing industry problems related to sediment treatment.

Characterizing free-living and particle-attached bacterial communities of a canyon river reservoir on the Yungui Plateau, China

Revealing the composition of free-living (FL) and particle-attached (PA) bacterial communities could provide insights into their distinct roles in biogeochemical processes and algal bloom dynamics. While there is still a lack of research about the difference and interactions between FL and PA communities, especially on the Yungui plateau with underestimated diversity. This study unveiled the structure of both FL and PA bacterial communities in a canyon reservoir (Wujiangdu) on the Yungui Plateau, southern China. Water samples were collected from surface water at nine sites in the reservoir. FL and PA bacterial community structures were identified by high-throughput 16S rRNA gene sequencing. We compared the structure and diversity of FL and PA bacteria and investigated their relationship with environmental factors. Results showed that there were different structures between FL and PA bacterial communities, and the dominant FL and PA phyla were affected by different environmental variables. Moreover, diversity of PA bacteria was greater than that of FL bacteria. Both groups exhibited distance decay patterns in this reservoir with varying correlations with geographic distances. FL fraction, however, exhibited a stronger correlation with environmental factors than the PA counterpart. Both FL and PA communities were phylogenetic clustering than expected according to the mean nearest taxon distance. This study provides fundamental information on FL and PA bacteria distribution and demonstrates how specific environmental factors affected these two bacterial fractions in canyon river reservoirs.

Glutamate Enhances Osmoadaptation of Anammox Bacteria under High Salinity: Genomic Analysis and Experimental Evidence

An osmoprotectant that alleviates the bacterial osmotic stress can improve the bioreactor treatment of saline wastewater. However, proposed candidates are expensive, and osmoprotectants of anammox bacteria and their ecophysiological roles are not fully understood. In this study, a comparative analysis of 34 high-quality public metagenome-assembled genomes from anammox bacteria revealed two distinct groups of osmoadaptation. Candidatus Scalindua and Kuenenia share a close phylogenomic relation and osmoadaptation gene profile and have pathways for glutamate transport and metabolisms for enhanced osmoadaptation. The batch assay results demonstrated that the reduced Ca. Kuenenia activity in saline conditions was substantially alleviated with the addition and subsequent synergistic effects of potassium and glutamate. The operational test of two reactors demonstrated that the reduced anammox performance under brine conditions rapidly recovered by 35.7-43.1% as a result of glutamate treatment. The Ca. Kuenenia 16S rRNA and hydrazine gene expressions were upregulated significantly (p < 0.05), and the abundance increased by approximately 19.9%, with a decrease in dominant heterotrophs. These data demonstrated the effectiveness of glutamate in alleviating the osmotic stress of Ca. Kuenenia. This study provides genomic insight into group-specific osmoadaptation of anammox bacteria and can facilitate the precision management of anammox reactors under high salinity.

An enhanced excess sludge fermentation process by anthraquinone-2-sulfonate as electron shuttles for the biorefinery of zero-carbon hydrogen

Excess sludge (ES) largely produced in municipal wastewater treatment plants is known as a waste biomass and the traditional treatment processes such as landfill and incineration are considered as unsustainable due to the negative environmental impact. Fermentation process of ES for the biorefinery of zero-carbon hydrogen has attracted an increasing interesting and was extensively researched in the last decades. However, the technology is far from commercial application due to the insufficient effectivity. In the present study, anthraquinone-2-sulfonate (AQS) as electron shuttles was introduced into the fermentation process of ES for mediating the composition and activity of bacterial community to get an enhanced biohydrogen production. Inoculated with the same anaerobic activated sludge of 1.12 gVSS/L, a series of batch anaerobic fermentation systems with various dosage of AQS were conducted at the same ES load of 2.75 gVSS/L, initial pH 6.5 and 35 °C. The results showed that the fermentation process was remarkably enhanced by the introduction of 100 mg/L AQS, accompanying the lag phase was shortened to 1.35 h from 7.62. The obtained biohydrogen yield and the specific biohydrogen production rate were also remarkably enhanced to 24.9 mL/gVSS and 0.3 mL/(gVSS·h), respectively. Illumina Miseq sequencing showed that Longilinea and Guggenheimella as the dominant genera had been enriched from 9.2% to 0-12.0% and 4.7%, respectively, in the presence of 100 mg/L AQS. Function predicted analysis suggested that the presence of AQS had increased the abundance of genes involved in the transport and metabolism of carbohydrate, amino acid and energy production. Further redundancy analysis (RDA) revealed that the enhanced hydrogen production was highly positively correlated with the enrichment of genera such as Longilinea and Guggenheimella. The research work presents a novel potential biorefinery of ES for the effective production of zero-carbon hydrogen.

Long-term effects of three compound probiotics on water quality, growth performances, microbiota distributions and resistance to Aeromonas veronii in crucian carp Carassius auratus gibelio

Probiotics could promote the healthy growth of aquatic animals and have been widely used in aquaculture. However, the influence of high concentration compound probiotics on the aquatic animals has not been reported. In the present study, a compound probiotics was used in high-density culture of crucian carps under the condition of micro-water exchange. During nearly 7-weeks feeding experiment, the aquaculture water quality, growth performances, disease resistance and microbiota distributions of crucian carps were tested. Under the high concentrations of compound probiotics, the content of total ammonia nitrogen and nitrite were finally in a state of dynamic equilibrium. The body length and weight of crucian carps in the experimental group (E) was significantly higher than that in the recirculating group (R). The antioxidant enzymes in the intestines and gills of the E group including SOD, CAT, GSH and MDA, were significantly higher than those in R group. The mortality of crucian carps in E group was significantly lower after the immersion infection of Aeromonas veronii. The addition of compound probiotics significantly increased the number of microorganisms detected in the intestines and gills of crucian carps in E group. The bacteria including Firmicutes, Planctomycetes, Verrucomicrobiota at the phylum level in E group were higher than those in R group. At the genus level, these bacteria (Pirellula, Roseimicrobium, Malikia) were not only higher in E group water, but also significantly higher in the intestines and gills than R group. The results of present study systematically analyzed the impact of high-concentration probiotics on crucian carps breeding, and speculated genus Pirellula, Roseimicrobium, Malikia may be used as aquatic probiotics. The present study will provide a new idea for the green and sustainable development of aquaculture.

Bacillus amyloliquefaciens FH-1 significantly affects cucumber seedlings and the rhizosphere bacterial community but not soil

Plant growth-promoting bacteria (PGPB) inoculants have been applied worldwide. However, the ecological roles of PGPB under different soil conditions are still not well understood. The present study aimed to explore the ecological roles of Bacillus amyloliquefaciens FH-1 (FH) on cucumber seedlings, rhizosphere soil properties, and the bacterial community in pot experiments. The results showed that FH had significant effects on cucumber seedlings and the rhizosphere bacterial community but not on soil properties. The FH promoted cucumber seedlings growth, reduced the rhizosphere bacterial diversity, increased Proteobacteria, and decreased Acidobacteria. Linear discriminant analysis (LDA) effect size (LEfSe) revealed that FH enriched two taxa (GKS2_174 and Nannocystaceae) and inhibited 18 taxa (mainly Acidobacteria, Actinobacteria, BRC1, Chloroflexi, Plantctomycetes, and Verrucomicrobia). Co-occurrence network analysis demonstrated that FH increased bacteria-bacteria interactions and that Bacillus (genus of FH) had few interactions with the enriched and inhibited taxa. This might indicate that FH does not directly affect the enriched and inhibited taxa. Correlation analysis results displayed that cucumber seedlings’ weight and height/length (except root length) were significantly correlated with the 18 inhibited taxa and the enriched taxa Nannocystaceae. It was speculated that FH might promote cucumber seedling growth by indirectly enriching Nannocystaceae and inhibiting some taxa from Acidobacteria, Actinobacteria, BRC1, Chloroflexi, Plantctomycetes, and Verrucomicrobia.

Assessment of the performance of an anoxic-aerobic microalgal-bacterial system treating digestate

The performance of an anoxic-aerobic microalgal-bacterial system treating synthetic food waste digestate at 10 days of hydraulic retention time via nitrification-denitrification under increasing digestate concentrations of 25%, 50%, and 100% (v/v) was assessed during Stages I, II and III, respectively. The system supported adequate treatment without external CO₂ supplementation since sufficient inorganic carbon in the digestate was available for autotrophic growth. High steady-state Total Organic Carbon (TOC) and Total Nitrogen (TN) removal efficiencies of 85-96% and 73-84% were achieved in Stages I and II. Similarly, PO₄^3--P removals of 81 ± 15% and 58 ± 4% were recorded during these stages. During Stage III, the average influent concentrations of 815 ± 35 mg TOC·L^-1, 610 ± 23 mg TN·L^-1, and 46 ± 11 mg PO₄^3--P·L^-1 induced O₂ limiting conditions, resulting in TOC, TN and PO₄^3--P removals of 85 ± 3%, 73 ± 3%, and 28 ± 16%, respectively. Digestate concentrations of 25% and 50% favored nitrification-denitrification mechanisms, whereas the treatment of undiluted digestate resulted in higher ammonia volatilization and hampered nitrification-denitrification. In Stages I and II, the microalgal community was dominated by Chlorella vulgaris and Cryptomonas sp., whereas Pseudoanabaena sp. was more abundant during Stage III. Illumina sequencing revealed the presence of carbon and nitrogen transforming bacteria, with dominances of the genera Gemmata, Azospirillum, and Psychrobacter during Stage I, II, and III, respectively. Finally, the high settleability of the biomass (98% of suspended solids removal in the settler) and average C (42%), N (7%), P (0.2%), and S (0.4%) contents recovered in the biomass confirmed its potential for agricultural applications, contributing to a closed-cycle management of food waste.

Large-scale switchable potentiostatically controlled/microbial fuel cell bioelectrochemical wastewater treatment system

The treatment of municipal wastewater is an energy-intensive process, with the delivery of oxygen as an electron acceptor accounting for a significant share of the total energy consumption. Microbial communities growing on polarized electrodes can facilitate wastewater treatment processes by exchanging electrons with the electrodes. As a new approach, we combined the use of polarized electrodes with microbial fuel cells (MFCs) to develop a switchable dual-mode bioelectrochemical wastewater treatment system. In this system, we first enriched microbial communities on polarized anodes and cathodes. After enrichment, the system was switched to either a self-powered MFC (SP-MFC) mode or a potentiostatically controlled (PC) mode. The system was evaluated at the laboratory scale (260 L, 4 anode and cathode pairs) and the pilot scale (1200 L, 16 anode and cathode pairs). PC and SP-MFC systems showed improved COD removal relative to control (41.6 ± 3.5 and 38.4 ± 3.1 vs 28.8 ± 2.1 mg L^-1 d^-1, respectively). The laboratory-scale system was operated without biological or electrical interruption for one year. Finally, specific enrichment of active microbial communities was observed on PC anodes in comparison to mixed-operation and non-polarized control anodes. The combined PC and SP-MFC systems allowed us to develop a sustainable and failure-free bioelectrochemical wastewater treatment system.

Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories

Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.

Simultaneous nitrogen and phosphorus removal by interactions between phosphate accumulating organisms (PAOs) and denitrifying phosphate accumulating organisms (DPAOs) in a sequencing batch reactor

The identification of phosphate-accumulating organisms (PAOs), denitrifying phosphate-accumulating organisms (DPAOs) and their relationship is a key pathway for optimizing nitrate and phosphate removal efficiency in activated sludge. In this study, the acclimatization of microorganisms in sequencing batch reactor were performed with anaerobic/aerobic (A/O) and anaerobic/anoxic (A/A) cycles, the biomass changes of PAOs and DPAOs and the correlations were then discussed. The results indicated that after acclimatization, the nutrient removal efficiencies reached to 85.34% (COD), 93.64% (PO₄^3--P) and 92.34% (NO₃^--N), respectively, with NO₃^--N:PO₄³-P of 1.5:1. The successful enrichment of PAOs and DPAOs (reached 97.9%) was verified by the change of relative metabolic activities, which was further proved by the change of bacterial diversity. The number of Candidatus Accumulibacter, Zoogloea, and Dechloromonas all increased at A/O and A/A stages while the number of Acinetobacter only increased at A/O stage. So Accumulibacter sp. was DPAO while Acinetobacter sp. was only PAO in this process, and genera Accumulibacter, Dechloromonas and Zoogloea greatly coordinated in denitrification and accumulating phosphorous though RDA and chord plot. This was worthy of attention and development to explore enhanced biological phosphorus removal (EBPR) in practical wastewater treatment via improving identification of bacterial species and symbiosis of bacteria community.

Determination of the bacterial microbiome of free-living amoebae isolated from wastewater by 16S rRNA amplicon-based sequencing

Free-living amoebae (FLA) are ubiquitous protozoa commonly found in water. FLA are well-established hosts for amoeba-resistant bacteria, most of which are pathogenic, and offer them shelter from adverse environmental conditions or water treatments. Since there is very little knowledge about the complete bacterial microbiome of FLA, in this work the bacterial microbiome of FLA isolated from wastewater both after secondary and tertiary treatments was studied by amplicon-based sequencing. FLA were detected in 87.5% and 50.0% of wastewater samples taken after secondary and tertiary disinfection treatments, respectively. The most abundant bacterial phyla were Proteobacteria, Planctomycetes, Bacteroidetes and Firmicutes, which represented 83.77% of the total bacterial FLA microbiome. The most abundant class of bacteria was Gammaproteobacteria, which contains an important number of relevant pathogenic bacteria. The bacteria of public health concern Aeromonas, Arcobacter, Campylobacter, Helicobacter, Klebsiella, Legionella, Mycobacterium, Pseudomonas and Salmonella were detected as part of the FLA microbiome. Although different microbial communities were identified in each sample, there is no correlation between the microbiome of FLA and the extent of wastewater treatment. To our knowledge, this is the first work in which the bacterial microbiome of FLA isolated from wastewater is studied. Obtained results indicate that FLA are hosts of potentially pathogenic bacteria in treated wastewater used for irrigation, which may pose a public health threat.

Understanding the Dependence of Micropollutant Biotransformation Rates on Short-Term Temperature Shifts

Temperature is a key factor that influences chemical biotransformation potential and rates, on which exposure and fate models rely to predict the environmental (micro)pollutant fate. Arrhenius-based models are currently implemented in environmental exposure assessment to adapt biotransformation rates to actual temperatures, assuming validity in the 0-30 °C range. However, evidence on how temperature shifts affect the physicochemical and microbial features in biological systems is scarce, questioning the validity of the existing modeling approaches. In this work, laboratory-scale batch assays were designed to investigate how a mixed microbial community responds to short-term temperature shifts, and how this impacts its ability to biotransform a range of structurally diverse micropollutants. Our results revealed three distinct kinetic responses at temperatures above 20 °C, mostly deviating from the classic Arrhenius-type behavior. Micropollutants with similar temperature responses appeared to undergo mostly similar initial biotransformation reactions, with substitution-type reactions maintaining Arrhenius-type behavior up to higher temperatures than oxidation-type reactions. Above 20 °C, the microbial community also showed marked shifts in both composition and activity, which mostly correlated with the observed deviations from Arrhenius-type behavior, with compositional changes becoming a more relevant factor in biotransformations catalyzed by more specific enzymes (e.g., oxidation reactions). Our findings underline the need to re-examine and further develop current environmental fate models by integrating biological aspects, to improve accuracy in predicting the environmental fate of micropollutants.

Nitrogen transformation processes and mass balance in deep constructed wetlands treating sewage, exploring the anammox contribution

This work was aimed to assess the contribution of classical nitrogen removal pathways in two deep constructed wetlands CW1 and CW2 located at Jaipur, India. Nitrogen mass balance revealed that 44.87% and 43.77% losses of T-N in CW1 and CW2 were unaccounted for. To elucidate these significant losses, the study was extended to assess the occurrence and contribution of a novel pathway (ANAMMOX) in overall nitrogen removal. The ratio of NH⁴⁺-N (removed) & NO₃^--N (produced) in CW1 & CW2 indicated that ANAMMOX could be one of the key pathways for nitrogen removal in the CWs besides nitrification-denitrification in microbial films. The molecular analysis confirmed bands of ANAMMOX bacteria developed intrinsically. The study revealed that deep wetlands can offer a feasible option for the sustenance of ANAMMOX bacteria and may help develop design parameters for CWs for achieving higherT-N removal withsimilarsurface area as that of conventional wetlands.

Planctomycetes as a Vital Constituent of the Microbial Communities Inhabiting Different Layers of the Meromictic Lake Sælenvannet (Norway)

Meromictic lakes are permanently stratified lakes that display steep gradients in salinity, oxygen and sulphur compounds tightly linked to bacterial community structure and diversity. Lake Sælenvannet is a meromictic lake located south of Bergen, Norway. The 26 m deep lake is connected to the open sea and permanently stratified into two layers separated by a chemocline. The upper water layer is brackish with major input from water runoff from the surroundings. The bottom layer consists of old saline water with low or no oxygen concentrations. Bacteria from phylum Planctomycetes are reported to be ubiquitous in lake environments. They are involved in the degradation of complex carbon sources in aquatic environments and are also linked to anaerobic processes such as fermentation and sulphur reduction. To study Planctomycete distribution along a chemical gradient, we sampled the water column throughout Lake Sælenvannet in 2012 and profiled the microbial community using 16S rRNA amplicon sequencing (metabarcoding) with 454 pyrosequencing. Planctomycetes related 16S rRNA gene sequences were found to be present both in the oxic and anoxic parts of the lake and showed an uneven distribution throughout the water column, with the highest relative abundance of 10% found in the saline anoxic layer at 15 m depth. In a follow-up study in 2014, samples from eight different depths were collected for enrichment and isolation of novel Planctomycetes. This study resulted in successful isolation in pure culture of 10 isolates affiliated to four different genera from the family Planctomycetaceae. One strain closely related to Blastopirellula cremea was isolated from 9 m depth, and two novel strains affiliated to the genera Stieleria and Gimesia were isolated at 7 and 9 m depths, respectively. Furthermore, seven isolates with identical 16S rRNA gene sequences were retrieved from seven different depths which varied greatly in salinity and chemical composition. These isolates likely represent a new species affiliated to Rubinisphaera. The adaptation of this novel Planctomycete to water depths spanning the entire chemical gradient could indicate a high phenotypic plasticity and/or a very efficient survival strategy. Overall, our results show the presence of a diverse group of Planctomycetes in Lake Sælenvannet, with a strong potential for novel adaptations to chemical stress factors.

Identifying the link between MBRs' key operating parameters and bacterial community: A step towards optimized leachate treatment

A MBR treating compost leachate was studied in order to link the operating parameters (solid and hydraulic retention time) to contaminant's specific bacterial catabolic activity. In this context, a lab-scale aerobic membrane bioreactor was operated for 200 days, at solid retention times (SRT) of 30 and 45 days and four different contaminant load rates. Results showed that increasing the food to microorganism ratio (F/M) by increasing the contaminant load rates lessened the selectivity pressure, which allowed the proliferation of subdominant operational taxonomic units (OTU) (relative abundance >3%) that were otherwise inhibited by highly adapted dominant OTUs (relative abundance >10%). Subsequently, increasing the SRT resulted in a lower species richness and the selection of two dominant types of bacteria: 1) genera with low growth rates that feed on non-limiting substrates or substrates with few competitors, and 2) genera with metabolisms that are highly specific to the available substrates and that can outcompete the other genera by using the substrate more efficiently. The bacterial population evolution observed during this study suggests that the mixed liquor population diversity and structure can be modulated with the operating conditions for the bioenhancement of contaminant specific catabolic activity. Identified dominant and subdominant genera were linked to the MBR's NH₄⁺ and COD removal performances. Interestingly, nitrification performances were unaffected by the organic load rate and the Nitrosomonas relative abundance.

Distinct Characteristics of Bacterial Community in the Soil of Nanshazhou Island, South China Sea

Characterizing soil bacterial community is important to understand microbial distribution affected by environmental factors. Here, we investigated the bacterial communities distributed from different location on Nanshazhou island, South China Sea. We collected and compared soil bacterial communities from central island, intertidal island, and inshore island. Results showed no difference in the bacterial richness and diversity for the soils from the three different locations. However, weighted and unweighted UniFrac distances analysis revealed that the three soil samples were clearly separated from each other. Five bacterial phyla, including Proteobacteria, Bacteroidetes, Verrucomicrobia, Spirochaetes and Tenericutes were more abundant in the inshore island sample; while Deinococcus-Thermus was more abundant in the intertidal island sample; and the central island sample had more abundant Gemmatimonadetes and Planctomycetes. Bacterial structure showed significantly positive relationships with organic matter content, but it was significantly negatively correlated with sodium content. Furthermore, a network analysis based on Spearman correlation coefficients showed that there were similar numbers of positive and negative correlations within the bacterial community of Nanshazhou island. Our results revealed that the soil bacterial communities in the three sampling sites were easily affected by environmental fluctuations.

Combined freezing-thawing pretreatment and microbial electrolysis cell for enhancement of highly concentrated organics degradation from dewatered sludge

The influence of freezing-thawing (F/T) pretreatment on the degradation of highly concentrated organic matters from dewatered sludge (DS) in microbial electrolysis cell (MEC) was investigated in this study. Extended freezing disintegrated the DS matrix and resulted in accelerated hydrolysis rate. The biogas production and stabilization were increased due to the pretreatment by 25–70% of H₂ production rate and 17.8–33.8% of COD reduction rate, respectively. Fourier transform infrared spectroscopy analysis indicated that the pretreatment was unable to alter the bioelectrochemical reactions except for accelerating degradation rate. Excitation and emission matrix (EEM) spectra showed that aromatic protein and soluble microbial products (SMPs)-like materials in DS were increasingly solubilized by the pretreatment and significantly removed during electrogenesis. The F/T-pretreated DS favored the enrichment of exoelectrogens in MEC.

Microbially influenced lacustrine carbonates: A comparison of Late Quaternary Lahontan tufa and modern thrombolite from Fayetteville Green Lake, NY

Carbonate microbialites in lakes can serve as valuable indicators of past environments, so long as the biogenicity and depositional setting of the microbialite can be accurately determined. Late Pleistocene to Early Holocene frondose draping tufa deposits from Winnemucca Dry Lake (Nevada, USA), a subbasin of pluvial Lake Lahontan, were examined in outcrop, petrographically, and geochemically to determine whether microbially induced precipitation is a dominant control on deposition. These observations were compared to modern, actively accumulating microbialites from Fayetteville Green Lake (New York, USA) using similar methods. In addition, preserved microbial DNA was extracted from the Lahontan tufa and sequenced to provide a more complete picture of the microbial communities. Tufas are texturally and geochemically similar to modern thrombolitic microbialites from Fayetteville Green Lake, and the stable isotopic composition of organic C, N, inorganic C, and O supports deposition associated with a lacustrine microbial mat environment dominated by photosynthetic processes. DNA extraction and sequencing indicate that photosynthetic microbial builders were present during tufa deposition, primarily Chloroflexi and Proteobacteria with minor abundances of Cyanobacteria and Acidobacteria. Based on the sequencing results, the depositional environment of the tufas can be constrained to the photic zone of the lake, contrasting with some previous interpretations that put tufa formation in deeper waters. Additionally, the presence of a number of mesothermophilic phyla, including Deinococcus-Thermus, indicates that thermal groundwater may have played a role in tufa deposition at sites not previously associated with groundwater influx. The interpretation of frondose tufas as microbially influenced deposits provides new context to interpretations of lake level and past environments in the Lahontan lake basins.

Lacipirellula parvula gen. nov., sp. nov., representing a lineage of planctomycetes widespread in low-oxygen habitats, description of the family Lacipirellulaceae fam. nov. and proposal of the orders Pirellulales ord. nov., Gemmatales ord. nov. and Isosphaerales ord. nov

Pirellula-like planctomycetes are ubiquitous aquatic bacteria, which are often detected in anoxic or micro-oxic habitats. By contrast, the taxonomically described representatives of these bacteria, with very few exceptions, are strict aerobes. Here, we report the isolation and characterization of the facultatively anaerobic planctomycete, strain PX69^T, which was isolated from a boreal lake. Its 16S rRNA gene sequence is affiliated with the Pirellula-related Pir4 clade, which is dominated by environmental sequences retrieved from a variety of low-oxygen habitats. Strain PX69^T was represented by ellipsoidal cells that multiplied by budding and grew on sugars, some polysaccharides and glycerol. Anaerobic growth occurred by means of fermentation. Strain PX69^T grew at pH 5.5–7.5 and at temperatures between 10 and 30 °C. The major fatty acids were C18:1ω9c, C16:0 and C16:1ω7c; the major intact polar lipid was dimethylphosphatidylethanolamine. The complete genome of strain PX69^T was 6.92 Mb in size; DNA G + C content was 61.7 mol%. Among characterized planctomycetes, the highest 16S rRNA gene similarity (90.4%) was observed with ‘Bythopirellula goksoyri’ Pr1d, a planctomycete from deep-sea sediments. We propose to classify PX69^T as a novel genus and species, Lacipirellula parvula gen. nov., sp. nov.; the type strain is strain PX69^T (=KCTC 72398^T = CECT 9826^T = VKM B-3335^T). This genus is placed in a novel family, Lacipirellulaceae fam. nov., which belongs to the order Pirellulales ord. nov. Based on the results of comparative genome analysis, we also suggest establishment of the orders Gemmatales ord. nov. and Isosphaerales ord. nov. as well as an emendation of the order Planctomycetales.

Molecular analysis of methanogen populations and their interactions within anaerobic sludge digesters

Knowledge of archaeal population structure, function and interactions is of great interest for a deeper understanding of the anaerobic digestion step in wastewater treatment process, that represents a bottle neck in the optimization of digesters performance. Although culture-independent techniques have enabled the exploration of archaeal population in such systems, their population dynamics and interactions still require further investigation. In the present study, 2646 almost full archaeal 16S rRNA gene sequences retrieved from 22 anaerobic digesters located worldwide were analyzed and classified into 83 Operational Taxonomic Units (OTUs) for Euryarchaeotes and 2 OTUs for Crenarchaeotes. Among the Euryarchaeotes, Methanosarcinales represent the predominant archaeal population (47.5% of total sequences), followed by the ARC I (WSA2) lineage (25.3%), Methanomicrobiales (19.9%) and Methanobacteriales (1.9%). Theses lineages are predominant in nine, five, two and one digesters respectively. However, the remaining 5 digesters show no predominance of any methanogenic group. According to the predominance of theses lineages, 5 digester profiles were distinguished. This study revealed a clear interaction between the 4 methanogenic lineages. A core of 12 OTUs represented by five, four, two and one OTU for Methanosarcinales, Methanomicrobiales, ARC I and Methanobacteriales respectively were quantitatively abundant in at least 50% of the analyzed digesters. 16S rRNA targeted hybridization oligonucleotide probes targeting the predominant OTUs are being developed to follow their population dynamics under various parameters.

The presence of in situ sulphamethoxazole degraders and their interactions with other microbes in activated sludge as revealed by DNA stable isotope probing and molecular ecological network analysis

Wastewater treatment plants (WWTPs) are the main hotspots for the release of antibiotics, including the widely used sulphonamides. Microbes play important roles in eliminating sulphonamides in WWTPs, and knowledge about these degraders and their interactions within the microbial community is crucial for operating and optimising WWTPs. In the present study, stable isotope probing (SIP) coupled with high-throughput sequencing as culture-independent approach revealed four operational taxonomic units (OTUs) involved in sulphamethoxazole (SMX) degradation in activated sludge. Except for the OTU affiliated with Gammaproteobacteria, the others have not been previously reported to possess the ability to metabolise SMX. The isolated SMX degrader by culture-dependent method did not participate in SMX biodegradation in situ according to the SIP analysis, and showed weak correlations with other members in the activated sludge. The complex interactions between in situ active SMX degraders and non-degrading microbes might explain our failure to isolate these degraders. In addition, sul1 genes associated with SMX resistance were also labelled with ¹³C, suggesting that they might benefit from SMX degradation and/or originate from the active SMX degraders. These findings broaden our understanding of the diversity of SMX-degrading microbes and their associated characteristics in WWTPs.

Treatment of Liquid Phase of Digestate from Agricultural Biogas Plant in a System with Aerobic Granules and Ultrafiltration

Management of digestate from manure co-digestion with a very high chemical oxygen demand (COD) to nitrogen ratio and high nitrogen loads are a major bottleneck in the development of agricultural biogas plants. The liquid phase of digestate mixed with municipal wastewater was treated in aerobic granular sludge batch reactors at cycle lengths (t) of 6 h (GSBR6h), 8 h (GSBR8h), and 12 h (GSBR12h), corresponding to nitrogen loads of 1.6, 1.2, and 0.8 g/(L·d). Thauera sp., Lacibacter sp., Thermanaerothrix sp., and Planctomyces sp. predominated in granules favoring effective granule formation and nitrogen removal. Increasing cycle lengths (t) significantly decreased proteins in soluble fraction of extracellular polymeric substances (EPS) in granules and increased polysaccharides in tightly bound EPS that resulted in higher granule diameters and higher COD removal. In GSBR6h, heterotrophic nitrification/denitrification was very efficient, but ammonium was fully oxidized in the last hour of the cycle. So in further studies, the effluent from GSBR8h was subjected to ultrafiltration (UF) at transmembrane pressures (TMPs) of 0.3, 0.4, and 0.5 MPa. A GSBR8h-UF system (TMP of 0.4 MPa) ensured full removal of total Kjeldahl nitrogen (TKN), suspended solids, and substantial reduction of COD and color with good permeate flux. The NOx-rich (about 250 mg/L), clear permeate can be reused in line with assumptions of modern circular economy.

Aquaponic Systems for Sustainable Resource Recovery: Linking Nitrogen Transformations to Microbial Communities

Aquaponics is a technology for food production (fish and vegetables/fruits) with concomitant remediation of nitrogen-rich aquaculture effluent. There is, however, a critical need to improve the nitrogen use efficiency (NUE) in aquaponics. Here, we employed quantitative polymerase chain reactions and next-generation sequencing to evaluate the bacterial communities and their links to nitrogen transformations for improving NUEs in four bench-scale plant-based floating-raft aquaponics (pak choi, lettuce, chive, and tomato) and three pH levels (7.0, 6.0, and 5.2). Low relative abundance of nitrifiers in plant roots and biofilters suggested nitrogen loss, which decreased NUE in aquaponics. Low pH level was a major factor that shifted the microbial communities and reduced the relative abundance of nitrifiers in aquaponic systems, leading to total ammonia nitrogen accumulation in recirculating water. In plant roots, the abundance of nitrite-oxidizing bacteria (e.g., Nitrospira spp.) did not decrease at low pH levels, suggesting the benefit of growing plants in aquaponics for efficient nitrification and improving NUE. These findings on microbial communities and nitrogen transformations provided complementary strategies to improve the performance of the aquaponics regarding water quality and extent of nutrient recovery from aquaculture effluent.

Identification of biphenyl-metabolising microbes in activated biosludge using cultivation-independent and -dependent approaches

Microbes have important roles in removing organic pollutants in wastewater treatment plants (WWTPs), especially in mineralising recalcitrant persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs). However, the majority of the microorganisms that metabolise these pollutants in situ remain elusive owing to barriers of traditional techniques in unravel yet-to-be-cultivated microbes. In this study, DNA stable-isotope probing (SIP) coupled with high-throughput sequencing was applied to identify the microbes responsible for PCB degradation in the activated biosludge of a WWTP using ¹³C-labelled biphenyl (BP). Results of time-course SIP revealed different bacteria and archaea involved in BP metabolism, which dominated the BP-degrading community at different time points. BP degradation by the genera Spartobacteria, Alicyclobacillus, Flavobacterium and the order Cenarchaeales has not been reported previously. The abundance of biphenyl dioxygenase (bphA) genes increased over time and a novel bphA gene was identified from the ¹³C-heavy DNA fraction. In addition, three cultivable BP degraders were isolated, but did not participate in BP degradation in situ or contain the identified bphA genes. Taken together, these data reveal the huge potential and important roles of yet-to-be-cultivated microbes responsible for PCB degradation in activated biosludge, providing fundamental knowledge on WWTP management to remove POPs.

Combined SHARON and ANAMMOX processes for ammoniacal nitrogen stabilisation in landfill bioreactors

Stabilisation of ammoniacal nitrogen from solid waste and leachate significantly improved by combining novel processes like SHARON (single reactor system for high activity ammonia removal over nitrite) and ANAMMOX (anaerobic ammonium oxidation) with advantages of lower carbon requirements, aeration and N₂O emissions. This paper deals with establishing combined SHARON-ANAMMOX processes in situ pilot-scale landfill bioreactors (LFBR). Molecular analysis in LFBR with changes in nitrogen, hydrazine, hydroxylamine confirmed aerobic and anaerobic ammonium oxidising bacteria (AOB & ANAMMOX) as key players in SHARON-ANAMMOX processes. In situ SHARON-ANAMMOX process was established in LFBR with total nitrogen and ammoniacal nitrogen removal efficiency of 84% and 71%, respectively at NLR of 1.2 kgN/m³/d in 147 d, compared to ammoniacal nitrogen removal of 49% at NLR of 1.0 kgNH₄-N/m³/d in 336 d feasible in Control LFBR. Nitrogen massbalance demonstrated in situ SHARON-ANAMMOX advantageous than control LFBR with higher nitrogen transformation to N₂ (50.8%) and lower residual nitrogen in solid waste (7.7%).

Development of simultaneous nitrification-denitrification (SND) in biofilm reactors with partially coupled a novel biodegradable carrier for nitrogen-rich water purification

Development of simultaneous nitrification-denitrification (SND) is a promising approach for nitrogen-rich water purification. Coupling biofilm reactors with novel biodegradable carrier of Pumelo Peel (PP) and various conventional plastic fillers (polyurethane filler, SPR-1 suspension filler, TA-II elastic filler and sphere filler) were examined to achieve SND in this study. Results represented that partially coupled with PP could achieve highly efficient SND. Optimal performance appealed in a bioreactor of coupling PP and SPR-1filler with ammonia and total nitrogen removal efficiencies of 96.8±4.0% and 78.9±9.5%, respectively, as well as low effluent COD_Mn of 1.85±0.86mgL^-1. Notably, PP and conventional plastic filler played obviously different roles in combined bioreactor system. Microbial analysis suggested that dominant genera were Thiothrix, Gemmata, unclassified comanonadaceae, unclassified Rhizobiales, Salipiger, Chloronema and Klebsiella in optimal combined bioreactor, which indicated novel co-existence of heterotrophic nitrification, solid-phase, non-solid-phase heterotrophic and sulfur-based autotrophic denitrification for achieving efficient SND.

The Paradigms They Are a-Changin': past, present and future of PVC bacteria research

These are exciting times for PVC researchers! The PVC superphylum is composed of the bacterial phyla Planctomycetes, Verrucomicrobia, Chlamydiae (those three founders giving it its name), Lentisphaerae and Kirimatiellaeota as well as some uncultured candidate phyla, such as the Candidatus Omnitrophica (previously known as OP3). Despite early debates, most of the disagreements that surround this group of bacteria have been recently resolved. In this article, we review the history of the study of PVC bacteria, with a particular focus on the misinterpretations that emerged early in the field and their resolution. We begin with a historical perspective that describes the relevant facts of PVC research from the early times when they were not yet termed PVC. Those were controversial times and we refer to them as the “discovery age” of the field. We continue by describing new discoveries due to novel techniques and data that combined with the reinterpretations of old ones have contributed to solve most of the discordances and we refer to these times as the “illumination age” of PVC research. We follow by arguing that we are just entering the “golden age” of PVC research and that the future of this growing community is looking bright. We finish by suggesting a few of the directions that PVC researches might take in the future.

Assessment of molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in different environmental samples using PCR primers based on 16S rRNA and functional genes

Eleven published PCR primer sets for detecting genes encoding 16S ribosomal RNA (rRNA), hydrazine oxidoreductase (HZO), cytochrome cd ₁-containing nitrite reductase (NirS), and hydrazine synthase subunit A (HzsA) of anaerobic ammonium-oxidizing (anammox) bacteria were assessed for the diversity and abundance of anammox bacteria in samples of three environments: wastewater treatment plant (WWTP), wetland of Mai Po Nature Reserve (MP), and the South China Sea (SCS). Consistent phylogenetic results of three biomarkers (16S rRNA, hzo, and hzsA) of anammox bacteria were obtained from all samples. WWTP had the lowest diversity with Candidatus Kuenenia dominating while the SCS was dominated by Candidatus Scalindua. MP showed the highest diversity of anammox bacteria including C. Scalindua, C. Kuenenia, and Candidatus Brocadia. Comparing different primer sets, no significant differences in specificity for 16S rRNA gene could be distinguished. Primer set CL1 showed relatively high efficiency in detecting the anammox bacterium hzo gene from all samples, while CL2 showed greater selectivity for WWTP samples. The recently reported primer sets of the hzsA gene resulted in high efficiencies in detecting anammox bacteria while nirS primer sets were more selective for specific samples. Results collectively indicate that the distribution of anammox bacteria is niche-specific within different ecosystems and primer specificity may cause biases on the diversity detected.

Epiphytic Planctomycetes communities associated with three main groups of macroalgae

Planctomycetes, a unique group of widespread and understudied bacteria, are known to be associated with macroalgae. The temporal dynamics and the host-specific association of planctomycetal communities on Fucus spiralis, Ulva sp. and Chondrus crispus from two locations in the North Coast of Portugal were assessed both by denaturing gradient gel electrophoresis with group-specific primers and 16S rDNA amplicon libraries. The epiphytic planctomycetal communities showed a significant association with the host macroalgal species independently of the geographical location and the season. This pattern was confirmed by clone libraries of winter and summer samples: we obtained 720 16S rRNA gene sequences that represented 44 operational taxonomic units (OTUs) within the phylum Planctomycetes. Most of the OTUs belonged to Blastopirellula, followed by Rhodopirellula, Planctomyces, the Pir4 lineage and the uncultured class OM190 (this last one nearly 30% of the OTUs). Ulva sp. and C. crispus had more diverse planctomycetal communities than F. spiralis. Analysis of beta diversity showed that the planctomycetal microbiome was host specific. We hypothesize that the specific association of Planctomycetes and their macroalgal hosts is likely determined by nutritional molecules provided by the algae and the set of sulfatases inherent to each Planctomycetes species.

A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam

Metagenomic approach was used to understand the structural and functional diversity present in arsenic contaminated groundwater of the Ganges Brahmaputra Delta aquifer system. A metagene dataset (coded as TTGW1) of 89,171 sequences (totaling 125,449,864 base pairs) with an average length of 1406 bps was annotated. About 74,478 sequences containing 101,948 predicted protein coding regions passed the quality control. Taxonomical classification revealed abundance of bacteria that accounted for 98.3% of the microbial population of the metagenome. Eukaryota had an abundance of 1.1% followed by archea that showed 0.4% abundance. In phylum based classification, Proteobacteria was dominant (62.6%) followed by Bacteroidetes (11.7%), Planctomycetes (7.7%), Verrucomicrobia (5.6%), Actinobacteria (3.7%) and Firmicutes (1.9%). The Clusters of Orthologous Groups (COGs) analysis indicated that the protein regulating the metabolic functions constituted a high percentage (18,199 reads; 39.3%) of the whole metagenome followed by the proteins regulating the cellular processes (22.3%). About 0.07% sequences of the whole metagenome were related to genes coding for arsenic resistant mechanisms. Nearly 50% sequences of these coded for the arsenate reductase enzyme (EC. 1.20.4.1), the dominant enzyme of ars operon. Proteins associated with iron acquisition and metabolism were coded by 2% of the metagenome as revealed through SEED analysis. Our study reveals the microbial diversity and provides an insight into the functional aspect of the genes that might play crucial role in arsenic geocycle in contaminated ground water of Assam.

Fimbriiglobus ruber gen. nov., sp. nov., a Gemmata-like planctomycete from Sphagnum peat bog and the proposal of Gemmataceae fam. nov

An aerobic, budding, dark pink to red-pigmented bacterium was isolated from an acidic boreal Sphagnum peat bog and designated strain SP5T. Cells of this strain were non-motile spheres that were uniformly covered with crateriform pits and fimbria, and tended to form aggregates during growth in liquid media. Strain SP5T was capable of growth between pH 4.0 and pH 6.8 (optimum at pH 5.5-6.0) and at temperatures between 10 and 30 °C (optimum at 20-25 °C). The preferred growth substrates were sugars and some heteropolysaccharides. The major fatty acids were C20 : 1ω9c, C16 : 1ω9c and C16 : 0, and the major polar lipid was trimethylornithine. Cells contained also significant amounts of bound (ω-1)OH-C30 : 1 fatty acid. The quinone was menaquinone-6, and the G+C content of the DNA was 60.7 mol%. Strain SP5T was a member of the order Planctomycetales and belonged to the phylogenetic lineage defined by the genus Gemmata. It displayed 88 and 89 % 16S rRNA gene sequence similarity to Gemmata obscuriglobusUQM 2246T and 'Gemmata massiliana' IIL30, 89 % to Zavarzinella formosa A10T and 86 % to Telmatocola sphagniphila SP2T. However, strain SP5T differed from members of these genera by cell morphology, substrate utilization pattern and fatty acid composition. Based on these data, the novel isolate should be considered as representing a novel species of a new genus of planctomycetes, for which the name Fimbriiglobus ruber gen. nov., sp. nov, is proposed. The type strain is SP5T (=LMG 29572T=VKM B-3045T). We also suggest the establishment of a novel family, Gemmataceaefam. nov., which includes the phylogenetically related genera Gemmata, Zavarzinella, Telmatocola and Fimbriiglobus.

Microbial Degradation of a Recalcitrant Pesticide: Chlordecone

Chlordecone (Kepone®) is a synthetic organochlorine insecticide (C₁₀Cl₁₀O) used worldwide mostly during the 1970 and 1980s. Its intensive application in the French West Indies to control the banana black weevil Cosmopolites sordidus led to a massive environmental pollution. Persistence of chlordecone in soils and water for numerous decades even centuries causes global public health and socio-economic concerns. In order to investigate the biodegradability of chlordecone, microbial enrichment cultures from soils contaminated by chlordecone or other organochlorines and from sludge of a wastewater treatment plant have been conducted. Different experimental procedures including original microcosms were carried out anaerobically over long periods of time. GC-MS monitoring resulted in the detection of chlorinated derivatives in several cultures, consistent with chlordecone biotransformation. More interestingly, disappearance of chlordecone (50 μg/mL) in two bacterial consortia was concomitant with the accumulation of a major metabolite of formula C₉Cl₅H₃ (named B1) as well as two minor metabolites C₁₀Cl₉HO (named A1) and C₉Cl₄H₄ (named B3). Finally, we report the isolation and the complete genomic sequences of two new Citrobacter isolates, closely related to Citrobacter amalonaticus, and that were capable of reproducing chlordecone transformation. Further characterization of these Citrobacter strains should yield deeper insights into the mechanisms involved in this transformation process.

Culture-Dependent and -Independent Identification of Polyphosphate-Accumulating Dechloromonas spp. Predominating in a Full-Scale Oxidation Ditch Wastewater Treatment Plant

The oxidation ditch process is one of the most economical approaches currently used to simultaneously remove organic carbon, nitrogen, and also phosphorus (P) from wastewater. However, limited information is available on biological P removal in this process. In the present study, microorganisms contributing to P removal in a full-scale oxidation ditch reactor were investigated using culture-dependent and -independent approaches. A microbial community analysis based on 16S rRNA gene sequencing revealed that a phylotype closely related to Dechloromonas spp. in the family Rhodocyclaceae dominated in the oxidation ditch reactor. This dominant Dechloromonas sp. was successfully isolated and subjected to fluorescent staining for polyphosphate, followed by microscopic observations and a spectrofluorometric analysis, which clearly demonstrated that the Dechloromonas isolate exhibited a strong ability to accumulate polyphosphate within its cells. These results indicate the potential key role of Dechloromonas spp. in efficient P removal in the oxidation ditch wastewater treatment process.

Biochemical Characterization of a Family 15 Carbohydrate Esterase from a Bacterial Marine Arctic Metagenome

Background

The glucuronoyl esterase enzymes of wood-degrading fungi (Carbohydrate Esterase family 15; CE15) form part of the hemicellulolytic and cellulolytic enzyme systems that break down plant biomass, and have possible applications in biotechnology. Homologous enzymes are predicted in the genomes of several bacteria, however these have been much less studied than their fungal counterparts. Here we describe the recombinant production and biochemical characterization of a bacterial CE15 enzyme denoted MZ0003, which was identified by in silico screening of a prokaryotic metagenome library derived from marine Arctic sediment. MZ0003 has high similarity to several uncharacterized gene products of polysaccharide-degrading bacterial species, and phylogenetic analysis indicates a deep evolutionary split between these CE15s and fungal homologs.

Results

MZ0003 appears to differ from previously-studied CE15s in some aspects. Some glucuronoyl esterase activity could be measured by qualitative thin-layer chromatography which confirms its assignment as a CE15, however MZ0003 can also hydrolyze a range of other esters, including p-nitrophenyl acetate, which is not acted upon by some fungal homologs. The structure of MZ0003 also appears to differ as it is predicted to have several large loop regions that are absent in previously studied CE15s, and a combination of homology-based modelling and site-directed mutagenesis indicate its catalytic residues deviate from the conserved Ser-His-Glu triad of many fungal CE15s. Taken together, these results indicate that potentially unexplored diversity exists among bacterial CE15s, and this may be accessed by investigation of the microbial metagenome. The combination of low activity on typical glucuronoyl esterase substrates, and the lack of glucuronic acid esters in the marine environment suggest that the physiological substrate of MZ0003 and its homologs is likely to be different from that of related fungal enzymes.

Gemmata species: Planctomycetes of medical interest

The Planctomycetes genus Gemmata is represented by both uncultured organisms and cultured Gemmata obscuriglobus and 'Gemmata massiliana' organisms. Their plasmidless 9.2 Mb genomes encode a complex cell plan, cell signaling capacities, antibiotic and trace metal resistance and multidrug resistance efflux pumps. As they lack iron metabolism pathways, they are fastidious. Gemmata spp. are mainly found in aquatic and soil environments but have also been found in hospital water networks in close proximity to patients, in animals, on human skin, the gut microbiota and in the blood of aplastic leukemic patients. Due to their panoply of attack and defense mechanisms and their recently demonstrated association with humans, the potential of Gemmata organisms to behave as opportunistic pathogens should be more widely recognized.

Bacterial ecology of abattoir wastewater treated by an anaerobic digestor

Wastewater from an anaerobic treatment plant at a slaughterhouse was analysed to determine the bacterial biodiversity present. Molecular analysis of the anaerobic sludge obtained from the treatment plant showed significant diversity, as 27 different phyla were identified. Firmicutes, Proteobacteria, Bacteroidetes, Thermotogae, Euryarchaeota (methanogens), and msbl6 (candidate division) were the dominant phyla of the anaerobic treatment plant and represented 21.7%, 18.5%, 11.5%, 9.4%, 8.9%, and 8.8% of the total bacteria identified, respectively. The dominant bacteria isolated were Clostridium, Bacteroides, Desulfobulbus, Desulfomicrobium, Desulfovibrio and Desulfotomaculum. Our results revealed the presence of new species, genera and families of microorganisms. The most interesting strains were characterised. Three new bacteria involved in anaerobic digestion of abattoir wastewater were published.

Draft genome of Gemmata massiliana sp. nov, a water-borne Planctomycetes species exhibiting two variants

Gemmata massiliana is a new Planctomycetes bacterium isolated from a hospital water network in France, using a new culture medium. It is an aerobic microorganism with optimal growth at pH 8, at 30 °C and salinity ≤ 1.25 % NaCl. G. massiliana is resistant to β-lactam antibiotics, due to lack of peptidoglycan in its cell wall.G. massiliana shares a 97 % 16S rRNA gene sequence similarity with the nearest species, Gemmata obscuriglobus; and 99 % similarity with unnamed soil isolates. Its 9,249,437-bp genome consists in one chromosome and no detectable plasmid and has a 64.07 % G + C content, 32.94 % of genes encoding for hypothetical proteins. The genome contains an incomplete 19.6-kb phage sequence, 26 CRISPRs, 3 CAS and 15 clusters of secondary metabolites. G. massiliana genome increases knowledge of a poorly known world of bacteria.

Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life

Background

Microbial genetic diversity is often investigated via the comparison of relatively similar 16S molecules through multiple alignments between reference sequences and novel environmental samples using phylogenetic trees, direct BLAST matches, or phylotypes counts. However, are we missing novel lineages in the microbial dark universe by relying on standard phylogenetic and BLAST methods? If so, how can we probe that universe using alternative approaches? We performed a novel type of multi-marker analysis of genetic diversity exploiting the topology of inclusive sequence similarity networks.

Results

Our protocol identified 86 ancient gene families, well distributed and rarely transferred across the 3 domains of life, and retrieved their environmental homologs among 10 million predicted ORFs from human gut samples and other metagenomic projects. Numerous highly divergent environmental homologs were observed in gut samples, although the most divergent genes were over-represented in non-gut environments. In our networks, most divergent environmental genes grouped exclusively with uncultured relatives, in maximal cliques. Sequences within these groups were under strong purifying selection and presented a range of genetic variation comparable to that of a prokaryotic domain.

Conclusions

Many genes families included environmental homologs that were highly divergent from cultured homologs: in 79 gene families (including 18 ribosomal proteins), Bacteria and Archaea were less divergent than some groups of environmental sequences were to any cultured or viral homologs. Moreover, some groups of environmental homologs branched very deeply in phylogenetic trees of life, when they were not too divergent to be aligned. These results underline how limited our understanding of the most diverse elements of the microbial world remains, and encourage a deeper exploration of natural communities and their genetic resources, hinting at the possibility that still unknown yet major divisions of life have yet to be discovered.

Reviewers

This article was reviewed by Eugene Koonin, William Martin and James McInerney.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-015-0092-3) contains supplementary material, which is available to authorized users.

Understanding the Linkage between Elevation and the Activated-Sludge Bacterial Community along a 3,600-Meter Elevation Gradient in China

To understand the relationship between elevation and bacterial communities in wastewater treatment plants (WWTPs), bacterial communities in 21 municipal WWTPs across China, located 9 to 3,660 m above sea level (masl), were investigated by 454 pyrosequencing. A threshold for the association of elevation with bacterial community richness and evenness was observed at approximately 1,200 masl. At lower elevations, both richness and evenness were not significantly associated with elevation. At higher elevations, significant declines with increased elevations were observed for community richness and evenness. The declining evenness trend at the phylum level was reflected by distinct trends in relative abundance for individual bacterial phyla. Betaproteobacteria, Bacteroidetes, and Firmicutes displayed significant increases, while most other phyla showed declines. Spearman correlation analysis indicated that the community richness and evenness at high elevations were more correlated with elevation than with any other single environmental variable. Redundancy analysis indicated that the contribution of elevation to community composition variances increased from 3% at lower elevations to 11% at higher elevations whereas the community composition variance at higher elevations remained much more explained by operational variables (39.2%) than by elevation. The influent total phosphorus concentration, food/microorganism ratio, and treatment process were the three shared dominant contributors to the community composition variance across the whole elevation gradient, followed by effluent ammonia nitrogen and temperature at higher elevations.

Long-term investigation of a novel electrochemical membrane bioreactor for low-strength municipal wastewater treatment

A novel and cost-effective electrochemical membrane bioreactor (EMBR) was proposed for low-strength wastewater treatment. In this system, influent organic matter could act as electron donor in the anode chamber and then denitrification was driven on the cathodes. During 270 days of operation, a positive and time-lag correlation was found between temperature and exoelectrogenesis process. At lower temperatures (<10∼15 °C), power production in the EMBR was negligible and therefore the integration did not improve the reactor performance. With the rebound of water temperatures over 15∼20 °C, efficient redox reactions were achieved in the EMBR, which subsequently resulted in sludge reduction (27.3% lower than the control MBR) and membrane fouling alleviation. Due to the capture of electrons that were then used at the cathode to drive the denitrification process, the total nitrogen removal efficiency of the EMBR averaged 78.2% at high temperatures, despite the decrease of organic loading rate of the feed for heterotrophic denitrification. Pyrosequencing revealed that the denitrifiers of Denitratisoma, Ottowia, Sulfuritalea and Thiobacillus were notably enriched in the cathode biofilm of the EMBR at high temperatures, and 6.05% of the sequences in the activated sludge were assigned into the denitrification related phylotypes, which was 65% higher compared to that of the control MBR. The enrichment of versatile nitrate/nitrite reducers could be conducive to the autotrophic and heterotrophic denitrification processes. Energy balance analysis also indicated that the total energy consumption of the EMBR was decreased by 20% compared to that of the CMBR (0.386 kWh/m(3) wastewater). Overall, the obtained results clearly demonstrate that this novel EMBR is capable of providing superior effluent quality, alleviating membrane fouling and incorporating into existing treatment facilities for improving the sustainability of wastewater treatment.

Co-occurence of Crenarchaeota, Thermoplasmata and methanogens in anaerobic sludge digesters

16S rRNA Crenarchaeota and Thermoplasmata sequences retrieved from 22 anaerobic digesters were analysed. 4.8 and 0.53 % of archaeal sequences were simultaneously affiliated to these lineages. A core of 2 operational taxonomic units (OTUs) representing 0.6 to -33.6 % of all archaeal sequences were defined for the Crenarchaeotes and identified to already known but not yet cultivable organisms in almost half of the digesters sampled. For the Thermoplasmata, apparently less abundant with 0.7 to -4.7 % of the archaeal sequences, 3 OTUs were identified. We showed here that Crenarchaeotes coexist with methanogens and are particularly abundant when Arch I lineage (also called WSA2 by Hugenholtz) is dominant in digesters. Moreover, Thermoplasmata were detected when Crenarchaeota were present. Interactions between methanogens, Crenarchaeotea and Thermoplamata were thus discussed.

Changing bacterial profile of Sundarbans, the world heritage mangrove: impact of anthropogenic interventions

Mangrove microbial communities and their associated activities have profound impact on biogeochemical cycles. Although microbial composition and structure are known to be influenced by biotic and abiotic factors in the mangrove sediments, finding direct correlations between them remains a challenge. In this study we have explored sediment bacterial diversity of the Sundarbans, a world heritage site using a culture-independent molecular approach. Bacterial diversity was analyzed from three different locations with a history of exposure to differential anthropogenic activities. 16S rRNA gene libraries were constructed and partial sequencing of the clones was performed to identify the microbial strains. We identified bacterial strains known to be involved in a variety of biodegradation/biotransformation processes including hydrocarbon degradation, and heavy metal resistance. Canonical Correspondence Analysis of the environmental and exploratory datasets revealed correlations between the ecological indices associated with pollutant levels and bacterial diversity across the sites. Our results indicate that sites with similar exposure of anthropogenic intervention reflect similar patterns of microbial diversity besides spatial commonalities.