Digging into the extracellular matrix of a complex microbial community using a combined metagenomic and metaproteomic approach

Deep insights into the biofilm formation mechanism and nitrogen-transformation network in a nitrate-dependent anaerobic methane oxidation biofilm

Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) process offers a promising solution for simultaneously achieving methane emissions reduction and efficient nitrogen removal in wastewater treatment. Although nitrogen removal at a practical rate has been achieved by n-DAMO biofilm process, the mechanisms of biofilm formation and nitrogen transformation remain to be elucidated. In this study, n-DAMO biofilms were successfully developed in the membrane aerated moving bed biofilm reactor (MAMBBR) and removed nitrate at a rate of 159 mg NO3--N L-1 d-1. The obvious increase in the content of extracellular polymeric substances (EPS) indicated that EPS production was important for biofilm development. n-DAMO microorganisms dominated the microbial community, and n-DAMO bacteria were the most abundant microorganisms. However, the expression of biosynthesis genes for proteins and polysaccharides encoded by n-DAMO archaea was significantly more active compared to other microorganisms, suggesting the central role of n-DAMO archaea in EPS production and biofilm formation. In addition to nitrate reduction, n-DAMO archaea were revealed to actively express dissimilatory nitrate reduction to ammonium and nitrogen fixation. The produced ammonium was putatively converted to dinitrogen gas through the joint function of n-DAMO archaea and n-DAMO bacteria. This study revealed the biofilm formation mechanism and nitrogen-transformation network in n-DAMO biofilm systems, shedding new light on promoting the application of n-DAMO process.

Matrix glycoconjugate characterization in multispecies biofilms and bioaggregates from the environment by means of fluorescently-labeled lectins

Environmental biofilms represent a complex mixture of different microorganisms. Their identity is usually analyzed by means of nucleic acid-based techniques. However, these biofilms are also composed of a highly complex extracellular matrix produced by the microbes within a particular biofilm system. The biochemical identity of this extracellular matrix remains in many cases an intractable part of biofilms and bioaggregates. Consequently, there is a need for an approach that will give access to the fully hydrated structure of the extracellular matrix or at least a major part of it. A crucial compound of the matrix identified as carbohydrate-based polymers represents major structural and functional constituents. These glycoconjugates can be characterized by using fluorescently-labeled lectins in combination with confocal laser scanning microscopy. The lectin approach is defined previously, as fluorescence lectin barcoding (FLBC) and fluorescence lectin-binding analysis (FLBA), where FLBC is equal to the screening of a particular sample with all the commercially available lectins and FLBA is the actual analysis of the matrix throughout an experiment with a selected panel of lectins. As the application of immune-based techniques in environmental biofilm systems is impossible, the lectin approach is currently the only option for probing lectin-specific glycoconjugates in complex biofilms and bioaggregates. From all the commercially available lectins tested, the lectins such as AAL, HAA, WGA, ConA, IAA, HPA, and LEA showed the highest binding efficiency. Furthermore, 20 of the overall lectins tested showed an intermediate signal intensity, nevertheless very useful for the assessment of matrix glycoconjugates. With the data compiled, we shall virtually shed more light on the dark matter of the extracellular matrix and their 3-dimensional distribution in environmental biofilm systems. The results will be helpful in future studies with a focus on the extracellular matrix glycoconjugates present in environmental microbial communities.

Advanced organic recovery from municipal wastewater with an enhanced magnetic separation (EMS) system: Pilot-scale verification

The up-concentration process has been demonstrated as an attractive approach to carbon-neutral wastewater treatment. Innovation in the separation processes can help eliminate the current heavy dependence on gravity, and credible pilot-scale verification is crucial for application promotion. We hereby proposed a pilot-scale enhanced magnetic separation (EMS) system as an up-concentration step to maximize energy recovery from municipal wastewater. The design of EMS was based on the hypothesis that magnetic-driven separation could be a breakthrough in separation speed, and adsorption could further enhance the separation efficiency by capturing soluble substances. Jar tests confirmed the feasibility of activated carbon adsorption, which could also roughen the surface of aggregates. Further, over one-year operation of a 300 m³/d EMS equipment provided optimum operation strategies and evidence of system effectiveness. More than 80% of particulate organics and 60% of soluble organics were removed within 10 min at an energy consumption of only 0.036 kWh/m³. The characteristics of sludge were clarified in terms of organic concentration, extracellular polymeric substances composition, and micro-community analysis. The anaerobic experiments further demonstrated the potential value of the concentrated products. Surprisingly, the developed EMS system exhibited significant advantages in time consumption and space occupation, with competitive operating cost and energy consumption. Overall, the results of this study posed the EMS process for up-concentration as a potential approach to organics recovery from municipal wastewater.

In-situ formation and self-immobilization of biogenic Fe oxides in anaerobic granular sludge for enhanced performance of acidogenesis and methanogenesis

Addition of ferric oxides into flocculent anaerobic sludge was reported to enhance methanogenesis due to accelerated direct interspecies electron transfer (DIET) between syntrophic microbial communities. However, it is generally hard to incorporate Fe oxides into already matured anaerobic granular sludge (AGS) due to its special aggregated structure. In this study, a novel method was attempted to fast incorporate Fe oxides into AGS through in-situ microbial formation and immobilization of biogenic Fe oxides. Factors influencing the formation of Fe oxides were investigated and effects of Fe oxides on the acidogenic and methanogenic performance of AGS were assessed. Results showed that AGS could form Fe oxides mainly in the form of magnetite and hematite through biological reduction of Fe(III) oxyhydroxide. A maximum loading amount of 83.9 mg Fe/g MLVSS was obtained at pH 7 after contacting with 60 mM Fe(III) oxyhydroxide. The efficiency of electron donors which supported Fe(III) reduction followed the order of pyruvate > propionate > glucose > acetate > lactate > formate. Addition of electron transfer mediators (ETMs) promoted the formation of Fe oxides and their performance followed the order of AQDS > AQC > humics > FMN > riboflavin. Presence of Fe oxides in AGS (134.6 Fe/g VSS) increased the production of volatile fatty acids (VFAs) and methane by 16.28% and 41.94% respectively, comparing to the control. The enhancement may be attributed to increased conductivity and stimulated growth of exoelectrogens (Clostridium and Anaerolinea) and methanogenic endoelectrogens Methanosaeta in granular sludge which may strengthen direct interspecies electron transfer between syntrophic microbial communities. Overall, this study provides an alternative strategy to improve the digestion performance of AGS through in-situ formation and immobilization of biogenic Fe oxides.

Application of extracellular polymers on soil communities exposed to oil and nickel contamination

The petrochemical industry is responsible for many accidental releases of pollutants in soil such as hydrocarbons and toxic metals. This co-contamination is responsible for a delay in the degradation of the organic pollution. Many successful technologies to remove these metals apply extracellular polymeric substances (EPS). In this study, we tested the application of an EPS from a Paenibacillus sp. to aid the bioremediation of soils contaminated with crude oil and nickel. We conducted a microcosm experiment to soils containing combinations of oil, nickel, and EPS. The final concentration of oil was evaluated with an infrared spectrometer. Also, we sequenced the metagenomes of the samples in an ion torrent sequencer. The application of EPS did not aid the removal of hydrocarbons with or without the presence of nickel. However, it led to a smaller decrease in the diversity indexes. EPS decreased the abundance of Actinobacteria and increased that of Proteobacteria. The EPS also decreased the connectivity among Actinobacteria in the network analysis. The results indicated that the addition of EPS had a higher effect on the community structure than nickel. Altogether, our results indicate that this approach did not aid the bioremediation of hydrocarbons likely due to its effect in the community structure that affected hydrocarbonoclastic microorganisms.

The Best-Practice Organism for Single-Species Studies of Antimicrobial Efficacy against Biofilms Is Pseudomonas aeruginosa

As potable water scarcity increases across the globe; it is imperative to identify energy and cost-effective processes for producing drinking-water from non-traditional sources. One established method is desalination of brackish and seawater via reverse osmosis (RO). However, the buildup of microorganisms at the water-membrane interface, known as biofouling, clogs RO membranes over time, increasing energy requirements and cost. To investigate biofouling mitigation methods, studies tend to focus on single-species biofilms; choice of organism is crucial to producing useful results. To determine a best-practice organism for studying antimicrobial treatment of biofilms, with specific interest in biofouling of RO membranes, we answered the following two questions, each via its own semi-systematic review: 1. Which organisms are commonly used to test antimicrobial efficacy against biofilms on RO membranes? 2. Which organisms are commonly identified via genetic analysis in biofilms on RO membranes? We then critically review the results of two semi-systematic reviews to identify pioneer organisms from the listed species. We focus on pioneer organisms because they initiate biofilm formation, therefore, inhibiting these organisms specifically may limit biofilm formation in the first place. Based on the analysis of the results, we recommend utilizing Pseudomonas aeruginosa for future single-species studies focused on biofilm treatment including, but not limited to, biofouling of RO membranes.

Membrane autopsy deciphering keystone microorganisms stubborn against online NaOCl cleaning in a full-scale MBR

The knowledge about membrane biofouling evolution in full-scale membrane bioreactor (MBR) applications is quite lacking, notwithstanding a few lab-scale investigations. For the first time, this study elaborated the effect of online NaOCl cleaning on the dynamic development of membrane biofilm microbiota during long-term operation of a large-scale MBR for municipal wastewater treatment (40,000 m³/d). Four times of membrane autopsies were conducted during 160 days operation to scrutinize the microbial community and concomitant organic foulants. The transmembrane pressure difference (TMP) development revealed limited effect of 30 min online NaOCl cleaning on long-term biofouling removal. NaOCl not only altered the structure of biofilm communities but also increased the richness and evenness on early fouling stages. Meanwhile, network analysis revealed the keystone taxa f_Comamonadaceae that played key roles in stabilizing community structure and developing anti-cleaning and irreversible fouling propensity of the biofilm. NaOCl cleaning also impacted the evolving of keystone taxa by intensifying the competition between the dominated taxa f_Moraxellaceae and other species during early fouling stages. Furthermore, the succession of the biofilm microbiota synchronously accelerated the TMP increase and the accumulation of organic foulants including polysaccharides, aromatic proteins and soluble microbial products during biofilm maturation. These identified key stubborn foulants shed light on limitations of current online NaOCl cleaning and provide guidance to optimize the efficiency of online chemical cleaning protocols in full-scale MBR operations.

Ratiometric Imaging of the in Situ pH Distribution of Biofilms by Use of Fluorescent Mesoporous Silica Nanosensors

Biofilms are communities of microorganisms enclosed in a self-generated matrix of extracellular polymeric substances. While biofilm recalcitrance and persistence are caused by several factors, a reduction in antimicrobial susceptibility has been closely associated with the generation of pH gradients within the biofilm structure. Cells embedded within the biofilm create a localized acidic microenvironment, which is unaffected by the external pH. Therefore, pH monitoring is a promising approach for understanding the complexities of a three-dimensional heterogeneous biofilm. A fluorescent pH nanosensor was designed through the synthesis of mesoporous silica nanoparticles (47 ± 5 nm diameter) conjugated to a pH-sensitive dye (fluorescein) and a pH-insensitive dye (rhodamine B) as an internal standard (dye-MSNs). The fluorescence intensity of fluorescein (I_F) reduced significantly as the pH was decreased from 8.5 to 3.5. In contrast, the fluorescence intensity of rhodamine B (I_R) remained constant at any pH. The ratio of I_F/I_R produced a sigmoidal curve with respect to the pH, in a working pH range between 4.5 and 7.5. Dye-MSNs enabled the measurement of pH gradients within Pseudomonas fluorescens WCS 365 biofilm microcolonies. The biofilms showed spatially distinct low-pH regions that were enclosed into large clusters corresponding to high-cell-density areas. Also present were small low-pH areas that spread indistinctly throughout the microcolony caused by the mass transfer effect. The lowest detected pH within the inner core of the microcolonies was 5.1, gradually increasing to a neutral pH toward the exterior of the microcolonies. The dye-MSNs were able to fully penetrate the biofilm matrix and allowed a quantitative ratiometric analysis of pH gradients and distribution throughout the biofilm, which was independent of the nanoparticle concentration.

Fluorescence Lectin Bar-Coding of Glycoconjugates in the Extracellular Matrix of Biofilm and Bioaggregate Forming Microorganisms

Microbial biofilm systems are defined as interface-associated microorganisms embedded into a self-produced matrix. The extracellular matrix represents a continuous challenge in terms of characterization and analysis. The tools applied in more detailed studies comprise extraction/chemical analysis, molecular characterization, and visualisation using various techniques. Imaging by laser microscopy became a standard tool for biofilm analysis, and, in combination with fluorescently labelled lectins, the glycoconjugates of the matrix can be assessed. By employing this approach a wide range of pure culture biofilms from different habitats were examined using the commercially available lectins. From the results, a binary barcode pattern of lectin binding can be generated. Furthermore, the results can be fine-tuned and transferred into a heat map according to signal intensity. The lectin barcode approach is suggested as a useful tool for investigating the biofilm matrix characteristics and dynamics at various levels, e.g. bacterial cell surfaces, adhesive footprints, individual microcolonies, and the gross biofilm or bio-aggregate. Hence fluorescence lectin bar-coding (FLBC) serves as a basis for a subsequent tailor-made fluorescence lectin-binding analysis (FLBA) of a particular biofilm. So far, the lectin approach represents the only tool for in situ characterization of the glycoconjugate makeup in biofilm systems.  Furthermore, lectin staining lends itself to other fluorescence techniques in order to correlate it with cellular biofilm constituents in general and glycoconjugate producers in particular.

Settling regimen transitions quantify solid separation limitations through correlation with floc size and shape

This study monitored three different activated sludge systems from the Blue Plains Advanced Wastewater Plant for a 1 year period to explore the relationship between effluent quality and activated sludge settling and flocculation behavior. Hindered settling rates (ISV) and sludge volume index (SVI) measurements were collected weekly. Novel metrics based on the solids concentration at which the transition between settling regimens occurred were also collected weekly. The transitional metrics were Threshold of Flocculation (TOF), and Limit of Stokesian Settling (LOSS). They marked the transition from discreet to flocculant settling, and from flocculant to hindered settling, respectively. A pilot clarifier and settling column were run and filmed to determine floc morphological properties. SVI was found to lose sensitivity (r < 0.20) when characterizing ISV above a hindered settling rate of 3 m h^-1. ISV and LOSS had a strong correlation (r = 0.71), but ISV was subject to change, depending on the solids concentration. Two sludge matrix limitations influencing effluent quality were characterized by transition concentrations; pinpoint floc formation, and loose floc formation. Pinpoint flocs had TOF values above 400 mg TSS L^-1; loose floc formation sludge had TOF and LOSS values below 400 mg TSS L^-1 and 900 mg TSS L^-1, respectively. TOF was found to correlate with the particle size distribution while LOSS correlated to the settling velocity distribution. The use of both TOF and LOSS is a quick and effective way to characterize limitations effecting effluent quality.

Metagenomes reveal microbial structures, functional potentials, and biofouling-related genes in a membrane bioreactor

Metagenomic sequencing was used to investigate the microbial structures, functional potentials, and biofouling-related genes in a membrane bioreactor (MBR). The results showed that the microbial community in the MBR was highly diverse. Notably, function analysis of the dominant genera indicated that common genes from different phylotypes were identified for important functional potentials with the observation of variation of abundances of genes in a certain taxon (e.g., Dechloromonas). Despite maintaining similar metabolic functional potentials with a parallel full-scale conventional activated sludge (CAS) system due to treating the identical wastewater, the MBR had more abundant nitrification-related bacteria and coding genes of ammonia monooxygenase, which could well explain its excellent ammonia removal in the low-temperature period. Furthermore, according to quantification of the genes involved in exopolysaccharide and extracellular polymeric substance (EPS) protein metabolism, the MBR did not show a much different potential in producing EPS compared to the CAS system, and bacteria from the membrane biofilm had lower abundances of genes associated with EPS biosynthesis and transport compared to the activated sludge in the MBR.

Enhancing metaproteomics--The value of models and defined environmental microbial systems

Metaproteomics--the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time--has provided new features to study complex microbial communities in order to unravel these "black boxes." New technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. Following a short introduction to microbial communities and metaproteomics, we introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.

A decade of metaproteomics: where we stand and what the future holds

We are living through exciting times during which we are able to unravel the “microbial dark matter” in and around us through the application of high‐resolution “meta‐omics”. Metaproteomics offers the ability to resolve the major catalytic units of microbial populations and thereby allows the establishment of genotype‐phenotype linkages from in situ samples. A decade has passed since the term “metaproteomics” was first coined and corresponding analyses were carried out on mixed microbial communities. Since then metaproteomics has yielded many important insights into microbial ecosystem function in the various environmental settings where it has been applied. Although initial progress in analytical capacities and resulting numbers of proteins identified was extremely fast, this trend slowed rapidly. Here, we discuss several representative metaproteomic investigations of activated sludge, acid mine drainage biofilms, freshwater and seawater microbial communities, soil, and human gut microbiota. By using these case studies, we highlight current challenges and possible solutions for metaproteomics to realize its full potential, i.e. to enable conclusive links between microbial community composition, physiology, function, interactions, ecology, and evolution in situ.

Characterization of the bacterial community involved in the bioflocculation process of wastewater organic matter in high-loaded MBRs

High-loaded membrane bioreactors (HL-MBRs), i.e., bioreactors equipped with a membrane for biomass retention and operated at extremely short sludge and hydraulic retention times, can concentrate sewage organic matter to facilitate subsequent energy and chemical recovery from these organics. Bioflocculation, accomplished by microorganisms that produce extracellular polymers, is a very important mechanism in these reactors. Bacterial diversity of the sludge and supernatant fraction of HL-MBRs operated at very short sludge retention times (0.125, 0.5, and 1 day) were determined using a PCR-denaturing gradient gel electrophoresis (DGGE) and clone library approach and compared to the diversity in sewage. Already at a sludge retention time (SRT) of 0.125 day, a distinct bacterial community developed compared to the community in sewage. Bioflocculation, however, was low and the majority of the bacteria, especially Arcobacter, were present in the supernatant fraction. Upon increasing SRT from 0.125 to 1 day, a much stronger bioflocculation was accompanied by an increased abundance of Bacteroidetes in the (solid) sludge fraction: 27.5 % at an SRT of 0.5 day and 46.4 % at an SRT of 1 day. Furthermore, cluster analysis of DGGE profiles revealed that the bacterial community structure in the sludge was different from that in the supernatant. To localize specific bacterial classes in the sludge flocs, fluorescence in situ hybridization (FISH) was carried out with three different bacterial probes. This showed that Betaproteobacteria formed clusters in the sludge flocs whereas Alphaproteobacteria and Gammaproteobacteria were mainly present as single cells.