Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy

Disentangling microbial niche balance and intermediates' trade-offs for anaerobic digestion stability and regulation

Anaerobic digestion (AD) is a key technology for converting organic matters to methane-rich biogas. However, nutrient imbalance can destabilize the whole digestion. To realize stable operation of AD and improve its efficiency, this work considers a new strategy to control the intermediate concentrations of poor AD under nutrient stress. For this purpose, long-term digestion under different nutrient conditions was investigated. Results showed that the feedstock with a low C/N ratio (= 6) caused VFA accumulation (2072 ± 632 mg/L), leading to the inhibition of methane production. Employing a substrate with a higher C/N ratio (= 11) and/or adding NH4HCO3 (200 mg NH4+-N/Ladd) could alleviate the VFA inhibition, but excessive dosage of NH4HCO3 would induce ammonia inhibition. Through the established digestion balance between free ammonia nitrogen (FAN) between 0 and 25 mg/L, volatile fatty acid (VFA) 510-2100 mg/L, and alkalinity (ALK) 3300-7800 mg/L, an efficient methane yield of 150-250 mL/g VS was achieved and stable operation of AD under nutrient stress (low C/N ratio) was realized. Metabolic reconstruction between Euryarchaeota sp. MAG162, Methanosarcina mazei MAG53 and Mesotoga infera MAG119 highlighted that microbial niche balance was developed as a result of digestion balance, which is beneficial for stable operation of AD. These findings improved our understanding of the interaction mechanism between intermediates and microbial niches for stability control in AD.

Recent Developments and Applications of Microbial Electrochemical Biosensors

This chapter provides a comprehensive overview of microbial electrochemical biosensors, which are a unique class of biosensors that utilize the metabolic activity of microorganisms to convert chemical signals into electrical signals. The principles and mechanisms of these biosensors are discussed, including the different types of microorganisms that can be used. The various applications of microbial electrochemical biosensors in fields such as environmental monitoring, medical diagnostics, and food safety are also explored. The chapter concludes with a discussion of future research directions and potential advancements in the field of microbial electrochemical biosensors.

Interactions among microorganisms functionally active for electron transfer and pollutant degradation in natural environments

Compared to single microbial strains, complex interactions between microbial consortia composed of various microorganisms have been shown to be effective in expanding ecological functions and accomplishing biological processes. Electroactive microorganisms (EMs) and degradable microorganisms (DMs) play vital roles in bioenergy production and the degradation of organic pollutants hazardous to human health. These microorganisms can strongly interact with other microorganisms and promote metabolic cooperation, thus facilitating electricity production and pollutant degradation. In this review, we describe several specific types of EMs and DMs based on their ability to adapt to different environments, and summarize the mechanism of EMs in extracellular electron transfer. The effects of interactions between EMs and DMs are evaluated in terms of electricity production and degradation efficiency. The principle of the enhancement in microbial consortia is also introduced, such as improved biomass, changed degradation pathways, and biocatalytic potentials, which are directly or indirectly conducive to human health.

Impacts of food waste to sludge ratios on microbial dynamics and functional traits in thermophilic digesters

A self-stabilizing microbial community lays the foundation of the efficient biochemical reactions of the anaerobic digestion (AD) process. Despite extensive profiling of microbial community dynamics under varying operating parameters, the effects of food waste (FW) to feeding sewage sludge (FSS) ratios on the microbial assembly, functional traits, and syntrophic interspecies interactions in thermophilic microbial consortia remain poorly understood. Here, we investigated the long-term impacts of the FW: FSS ratio on the thermophilic AD microbiome using genome-centric metagenomics. Both the short reads (SRs) assembly, and the iterative hybrid assembly (IHA) of SRs and nanopore long reads (LRs) were used to reconstruct metagenome-assembled genomes (MAGs) and four microbial clusters were identified, demonstrating different microbial dynamics patterns in response to varying FW:FSS ratios. Cluster C1-C3 were comprised of full functional members with genetic potentials in fulfilling empirical AD biochemical reactions, wherein, syntrophic decarboxylating acetogens could interact with methanogens, and some microbes could be energized by the electron bifurcation mechanism to drive thermodynamics unfavorable reactions. We found the co-existence of both acetogenic and hydrogenotrophic methanogens in the AD microbiome, and they altered their trophic groups to scavenge the methanogenic substrates in ensuring the methane generation in digesters with different FW:FSS ratios. Another interesting observation was that two phylogenetically close Thermotogota species showed a possible strong competition on carbon source inferred by the nearly complete genetic overlap of their relevant pathways.

Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation

Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.

Biofilm Biology and Engineering of Geobacter and Shewanella spp. for Energy Applications

Geobacter and Shewanella spp. were discovered in late 1980s as dissimilatory metal-reducing microorganisms that can transfer electrons from cytoplasmic respiratory oxidation reactions to external metal-containing minerals. In addition to mineral-based electron acceptors, Geobacter and Shewanella spp. also can transfer electrons to electrodes. The microorganisms that have abilities to transfer electrons to electrodes are known as exoelectrogens. Because of their remarkable abilities of electron transfer, Geobacter and Shewanella spp. have been the two most well studied groups of exoelectrogens. They are widely used in bioelectrochemical systems (BESs) for various biotechnological applications, such as bioelectricity generation via microbial fuel cells. These applications mostly associate with Geobacter and Shewanella biofilms grown on the surfaces of electrodes. Geobacter and Shewanella biofilms are electrically conductive, which is conferred by matrix-associated electroactive components such as c-type cytochromes and electrically conductive nanowires. The thickness and electroactivity of Geobacter and Shewanella biofilms have a significant impact on electron transfer efficiency in BESs. In this review, we first briefly discuss the roles of planktonic and biofilm-forming Geobacter and Shewanella cells in BESs, and then review biofilm biology with the focus on biofilm development, biofilm matrix, heterogeneity in biofilm and signaling regulatory systems mediating formation of Geobacter and Shewanella biofilms. Finally, we discuss strategies of Geobacter and Shewanella biofilm engineering for improving electron transfer efficiency to obtain enhanced BES performance.

Anodic and cathodic biofilms coupled with electricity generation in single-chamber microbial fuel cell using activated sludge

Microbial fuel cell (MFC) is used to remove organic pollutants while generating electricity. Biocathode plays as an efficient electrocatalyst for accelerating the Oxidation Reduction Reaction (ORR) of oxygen in MFC. This study integrated biocathode into a single-chamber microbial fuel cell (BSCMFC) to produce electricity from an organic substrate using aerobic activated sludge to gain more insights into anodic and cathodic biofilms. The maximum power density, current density, chemical oxygen demand (COD) removal, and coulombic efficiency were 0.593 W m^-3, 2.6 A m^-3, 83 ± 8.4%, and 22 ± 2.5%, respectively. Extracellular polymeric substances (EPS) produced by biofilm from the biocathode were higher than the bioanode. Infrared spectroscopy and Scanning Electron Microscope (SEM) examined confirmed the presence of biofilm by the adhesion on electrodes. The dominant phyla in bioanode were Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, while the dominant phylum in the biocathode was Proteobacteria. Therefore, this study demonstrates the applicable use of BSCMFC for bioelectricity generation and pollution control.

Potential of cyanobacteria in the conversion of wastewater to biofuels

Environmental and energy security has now become a serious global problem, requiring a lot of research to find and implement its cost-effective and environmentally friendly alternatives. The development and use of renewable energy sources is necessary and important in order to avoid the emergence of a global economic crisis. One of the solution to prevent a future crisis caused by energy shortages is to introduce biofuels into the fuel market. Despite the fact that various forms of renewable energy are currently used, the prospects for the production of biofuels from cyanobacteria are quite high due to their unique properties, such as a high lipid content and a suitable fatty acid (FA) composition for the production of biofuels, their suitability for growing open water and the ability to grow on wastewater. The purpose of this article is to provide a comprehensive overview of the potential of cyanobacteria in the conversion of wastewater into biofuels. The article covers comparative data on the accumulation of lipids and the content of fatty acids in various representatives of cyanobacteria and their possibilities in the remediation of wastewater. Various approaches to the extraction of lipids from phototrophic microorganisms that are currently available, their advantages and disadvantages, and the results of the monitoring of the main key points of the development of the technology for converting cyanobacterial biomass into biofuels, with an emphasis on the existing barriers, effects and solutions, are also considered. Further research in this field is required for the successful implementation of this technology on an industrial scale.

Microbial fuel cells: a comprehensive review for beginners

Microbial fuel cells (MFCs) have shown immense potential as a one-stop solution for three major sustainability issues confronting the world today-energy security, global warming and wastewater management. MFCs represent a cross-disciplinary platform for research at the confluence of the natural and engineering sciences. The diversity of variables influencing performance of MFCs has garnered research interest across varied scientific disciplines since the beginning of this century. The increasing number of research publications has made it necessary to keep track of work being carried out by research groups across the globe and consolidate significant findings on a regular basis. Review articles are often the nodal points for beginners who are required to undertake an exploratory survey of literature to identify a suitable research problem. This 'review of reviews' is a ready-reckoner that directs readers to relevant reviews and research articles reporting significant developments in MFC research in the last two decades. The article also highlights the areas needing research attention which when addressed could take this technology a few more steps closer to practical implementation.

Mo2 C/Reduced Graphene Oxide Composites with Enhanced Electrocatalytic Activity and Biocompatibility for Microbial Fuel Cells

A simple, cost-effective strategy was developed to effectively improve the electron transfer efficiency as well as the power output of microbial fuel cells (MFCs) by decorating the commercial carbon paper (CP) anode with an advanced Mo₂ C/reduced graphene oxide (Mo₂ C/RGO) composite. Benefiting from the synergistic effects of the superior electrocatalytic activity of Mo₂ C, the high surface area, and prominent conductivity of RGO, the MFC equipped with this Mo₂ C/RGO composite yielded a remarkable output power density of 1747±37.6 mW m^-2 , which was considerably higher than that of CP-MFC (926.8±6.3 mW m^-2 ). Importantly, the composite also facilitated the formation of 3D hybrid biofilm and could effectively improve the bacteria-electrode interaction. These features resulted in an enhanced coulombic efficiency up 13.2 %, nearly one order of magnitude higher than that of the CP (1.2 %).

In Silico Study of the Structure and Ligand Interactions of Alcohol Dehydrogenase from Cyanobacterium Synechocystis Sp. PCC 6803 as a Key Enzyme for Biofuel Production

Alcohol dehydrogenase is one of the most critical enzymes in the production of ethanol and butanol. Synechocystis sp. PCC 6803 is a model cyanobacterium organism that is able to produce alcohols through its autotrophic energy production system. In spite of the high potential for biofuel production by this bacteria, the structure of its alcohol dehydrogenase has not been subjected to in-depth studies. The current study was aimed to analyze the molecular model for alcohol dehydrogenase of Synechocystis sp. PCC 6803 and scrutinize the interactions of different chemicals, including substrates and coenzymes. Also, the phylogenetic tree was provided to investigate the relation between different sources. The results indicated that alcohol dehydrogenase of Synechocystis sp. PCC 6803 has a different sequence compared with other Alcohol dehydrogenases (ADHs) of cyanobacterial family members. Verification of the homology model using Ramachandran plot by PROCHECK indicated that all of the residues are in favored or allowed regions of the plot. This enzyme has two Zn ions in its structure which is very similar to the other Zn-dependent ADHs. Docking studies suggest that this enzyme could have more active sites for different substrates. In addition, this enzyme has more affinity to NADH as a cofactor and sinapaldehyde as a substrate compared with the other cofactor and substrates.

Cheese whey to biohydrogen and useful organic acids: A non-pathogenic microbial treatment by L. acidophilus

The burgeoning organic waste and continuously increasing energy demands have resulted in significant environmental pollution concerns. To address this issue, the potential of different bacteria to produce biogas/biohydrogen from organic waste can be utilized as a source of renewable energy, however these pathogenic bacteria are not safe to use without strict contact isolation. In this study the role of safe food grade lactic acid bacteria (Lactobacillus spp.) was investigated for production of biogas from cheese waste with starting hexose concentration 32 g/L. The bacterium Lactobacillus acidophilus was identified as one of the major biogas producers at optimum pH of 6.5. Further the optimum inoculum conditions were found to be 12.5% at inoculum age of 18 h. During the investigation the maximum biogas production was observed to be 1665 mL after 72 hours of incubation at pH 6.5. The biogas production was accompanied with production of other valuable metabolites in the form of organic acids including pyruvate, propionate, acetate, lactate, formate and butyrate. Thus this research is paving way for nonpathogenic production of biohydrogen from food waste.

Syntroph diversity and abundance in anaerobic digestion revealed through a comparative core microbiome approach

Anaerobic digestion is an important biotechnology treatment process for conversion of waste to energy. In this study, a comparative core microbiome approach, i.e., determining taxa that are shared in functioning digesters but not shared in non-functioning digesters, was used to determine microbial taxa that could play key roles for effective anaerobic digestion. Anaerobic digester functions were impaired by adding the broad-spectrum antimicrobial triclosan (TCS) or triclocarban (TCC) at different concentrations, and the core microbiomes in both functioning and non-functioning anaerobic digesters were compared. Digesters treated with high (2500 mg/kg) or medium (450 mg/kg) TCS and high (850 mg/kg) TCC concentrations lost their function, i.e., methane production decreased, effluent volatile fatty acid concentrations increased, and pH decreased. Changes in microbial community diversity and compositions were assessed using 16S rRNA gene amplicon sequencing. Microbial richness decreased significantly in non-functioning digesters (p < 0.001). Microbial community compositions in non-functioning digesters significantly differed from those in functioning digesters (p = 0.001, ANOSIM). Microbes identified as potentially key taxa included previously known fatty acid-degrading syntrophs and amino acid-degrading syntrophs. A diverse group of syntrophs detected in this study had low relative abundance in functioning digesters, suggesting the importance of rare microbes in anaerobic digester operation. The comparative microbiome approach used in this study can be applied to other microbial systems where a community-driven biological phenomena can be observed directly.

Novel ecological insights and functional roles during anaerobic digestion of saccharides unveiled by genome-centric metagenomics

In typical anaerobic digestion (AD) systems, the microbial functional assertion is hampered by synchronised versatile metabolism required for heterogeneous substrates degradation. Thus, the intricate methanogenic process from organic compounds remains an enigma after decades of empirical operation. In this study, simplified AD microbial communities were obtained with substrate specifications and continuous reactor operation. Genome-centric metagenomic approach was followed to holistically investigate the metabolic pathways of the AD and the microbial synergistic networks. In total, 63 metagenome assembled genomes (MAGs) were assembled from 8 metagenomes acquired in specific methanogenic niches. The metabolic pathways were reconstructed from the annotated genes and their dynamicity under experimental conditions. The results show that the methanogenic niches nourish unique metabolism beyond current knowledge acquired from cultivation-based methods. A novel glucose mineralization model without acetate formation was proposed and asserted in a pair of syntrophs: Clostridiaceae sp. and Methanoculleus thermophilus. Moreover, the catabolic pathway was elucidated in uncharacterized syntrophic acetate oxidizers, Synergistaceae spp. A remarkable evolutionary insight is the discovery that electron transport and energy conservation mechanisms impose selective pressure on syntrophic partners. Overall, the functional roles of the individual microbes tightly rely on the catabolic pathways and cannot always be physiologically defined in accordance with conventional four-step AD concept. The substrate-specific systems provided a traceable microbial community to dissecting the AD process. The genome-centric metagenomics successfully constructed genomes of microbes that have not been previously isolated and illustrated metabolic pathways that beyond the current knowledge of AD process. This study provides new perspectives to unravel the AD microbial ecology and suggests more attention should be paid on uncharacterized metabolism specifically harboured by AD microbial communities.

Anodic microbial community analysis of microbial fuel cells based on enriched inoculum from freshwater sediment

The characterization of anodic microbial communities is of great importance in the study of microbial fuel cells (MFCs). These kinds of devices mainly require a high abundance of anode respiring bacteria (ARB) in the anode chamber for optimal performance. This study evaluated the effect of different enrichments of environmental freshwater sediment samples used as inocula on microbial community structures in MFCs. Two enrichment media were compared: ferric citrate (FeC) enrichment, with the purpose of increasing the ARB percentage, and general enrichment (Gen). The microbial community dynamics were evaluated by polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE) and real time polymerase chain reaction (qPCR). The enrichment effect was visible on the microbial community composition both during precultures and in anode MFCs. Both enrichment approaches affected microbial communities. Shannon diversity as well as β-Proteobacteria and γ-Proteobacteria percentages decreased during the enrichment steps, especially for FeC (p < 0.01). Our data suggest that FeC enrichment excessively reduced the diversity of the anode community, rather than promoting the proliferation of ARB, causing a condition that did not produce advantages in terms of system performance.

Managing microbial communities in membrane biofilm reactors

Membrane biofilm reactors (MBfRs) deliver gaseous substrates to biofilms that develop on the outside of gas-transfer membranes. When an MBfR delivers electron donors hydrogen (H₂) or methane (CH₄), a wide range of oxidized contaminants can be reduced as electron acceptors, e.g., nitrate, perchlorate, selenate, and trichloroethene. When O₂ is delivered as an electron acceptor, reduced contaminants can be oxidized, e.g., benzene, toluene, and surfactants. The MBfR's biofilm often harbors a complex microbial community; failure to control the growth of undesirable microorganisms can result in poor performance. Fortunately, the community's structure and function can be managed using a set of design and operation features as follows: gas pressure, membrane type, and surface loadings. Proper selection of these features ensures that the best microbial community is selected and sustained. Successful design and operation of an MBfR depends on a holistic understanding of the microbial community's structure and function. This involves integrating performance data with omics results, such as with stoichiometric and kinetic modeling.

Meta-proteomic analysis of protein expression distinctive to electricity-generating biofilm communities in air-cathode microbial fuel cells

BACKGROUND

Bioelectrochemical systems (BESs) harness electrons from microbial respiration to generate power or chemical products from a variety of organic feedstocks, including lignocellulosic biomass, fermentation byproducts, and wastewater sludge. In some BESs, such as microbial fuel cells (MFCs), bacteria living in a biofilm use the anode as an electron acceptor for electrons harvested from organic materials such as lignocellulosic biomass or waste byproducts, generating energy that may be used by humans. Many BES applications use bacterial biofilm communities, but no studies have investigated protein expression by the anode biofilm community as a whole.

RESULTS

To discover functional protein expression during current generation that may be useful for MFC optimization, a label-free meta-proteomics approach was used to compare protein expression in acetate-fed anode biofilms before and after the onset of robust electricity generation. Meta-proteomic comparisons were integrated with 16S rRNA gene-based community analysis at four developmental stages. The community composition shifted from dominance by aerobic Gammaproteobacteria (90.9 ± 3.3%) during initial biofilm formation to dominance by Deltaproteobacteria, particularly Geobacter (68.7 ± 3.6%) in mature, electricity-generating anodes. Community diversity in the intermediate stage, just after robust current generation began, was double that at the early stage and nearly double that of mature anode communities. Maximum current densities at the intermediate stage, however, were relatively similar (~ 83%) to those achieved by mature-stage biofilms. Meta-proteomic analysis, correlated with population changes, revealed significant enrichment of categories specific to membrane and transport functions among proteins from electricity-producing biofilms. Proteins detected only in electricity-producing biofilms were associated with gluconeogenesis, the glyoxylate cycle, and fatty acid β-oxidation, as well as with denitrification and competitive inhibition.

CONCLUSIONS

The results demonstrate that it is possible for an MFC microbial community to generate robust current densities while exhibiting high taxonomic diversity. Moreover, these data provide evidence to suggest that startup growth of air-cathode MFCs under conditions that promote the establishment of aerobic-anaerobic syntrophy may decrease startup times. This study represents the first investigation into protein expression of a complex BES anode biofilm community as a whole. The findings contribute to understanding of the molecular mechanisms at work during BES startup and suggest options for improvement of BES generation of bioelectricity from renewable biomass.

Microbial characteristics analysis and kinetic studies on substrate composition to methane after microbial and nutritional regulation of fruit and vegetable wastes anaerobic digestion

This study firstly evaluated the microbial role when choosing the acclimated anaerobic granular sludge (AGS) and waste activated sludge (WAS) as microbial and nutritional regulators to improve the biomethanation of fruit and vegetable wastes (FVW). Results showed that the enriched hydrogenotrophic methanogens, and Firmicutes and Spirochaeta in the AGS were responsible for the enhanced methane yield. A synthetic waste representing the mixture of WAS and FVW was then used to investigate the influences of different substrate composition on methane generations. The optimal mass ratio of carbohydrate/protein/cellulose was observed to be 50:45:5, and the corresponding methane yield was 411mL/g-VS_added. Methane kinetic studies suggested that the modified Gompertz model fitted better with those substrates of carbohydrate- than protein-predominated. Parameter results indicated that the maximum methane yield and production rate were enhanced firstly and then reduced with the decreasing carbohydrate and increasing protein percentages; the lag phase time however increased continuously.

Microbial diversity structure in acetate single chamber microbial fuel cell for electricity generation

This study investigates the performance of acetate feed membrane less single chamber microbial fuel cell and physical characterization of the bio film present on the anode surface using Scanning Electron Microscope (SEM) and 16S rRNA analyzer. The performance has been investigated using Teflon treated carbon paper with 0.3 mg/cm2 Pt/C loaded as a cathode and carbon paper as an anode. The maximum open circuit potential is noticed as 791 mV, the system successfully revealed a maximum power density of 86.1 mW m-2 at stable current density of 354 mA m-2 with high coulombic efficiency of 65% at maximum degradation rate of 96%. SEM showed the dense adherence of microorganisms on the anode. 16S rRNA sequencing results indicates phylogenetic mixture in the communities of anodic biofilm and there is no single dominant bacterial species. The dominant phyla are Firmicutes, Gamma Proteobacteria, Alpha Proteobacteria, Actinobacteria, with ten dominant microbial strains: Bacillus firmus, Shewanella profunda, Bacillus isronensis, Brevundimonas bullata, Pseudomonas putida, Planococcus citreus, Micrococcus endophyticus, Acinetobacter tandoii, Bacillus safensis and Shewanella xiamenensis.

Identification and characterization of a symbiotic alga from soil bryophyte for lipid profiles

A symbiotic alga was successfully isolated from the soil moss Entodon obtusatus found in the Guandi Mountains, Shanxi Province, China, and cultivated under axenic conditions. Morphological observations showed that the symbiotic alga was similar to Chlorococcum Based on phylogenetic analysis of 18S rRNA and rbcL genes and internal transcribed spacer (ITS) regions, Chlorococcum sp. GD was identified as Chlorococcum sphacosum The three data sets were congruent for those aspects of the topologies that were relatively robust, and differed for those parts of the topologies that were not. This strain was cultured in BG11 medium to test its growth and biodiesel properties. It produced a lipid content of nearly 40%, and achieved biomass concentration of 410 mg l(-1) and lipid productivity of 6.76 mg l(-1) day(-1), with favorable C16:0 (23.10%) and C18:1 (21.62%) fatty acid content. This alga appears to have potential for use in biodiesel production.

Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks

Peptide and protein identification remains challenging in organisms with poorly annotated or rapidly evolving genomes, as are commonly encountered in environmental or biofuels research. Such limitations render tandem mass spectrometry (MS/MS) database search algorithms ineffective as they lack corresponding sequences required for peptide-spectrum matching. We address this challenge with the spectral networks approach to (1) match spectra of orthologous peptides across multiple related species and then (2) propagate peptide annotations from identified to unidentified spectra. We here present algorithms to assess the statistical significance of spectral alignments (Align-GF), reduce the impurity in spectral networks, and accurately estimate the error rate in propagated identifications. Analyzing three related Cyanothece species, a model organism for biohydrogen production, spectral networks identified peptides from highly divergent sequences from networks with dozens of variant peptides, including thousands of peptides in species lacking a sequenced genome. Our analysis further detected the presence of many novel putative peptides even in genomically characterized species, thus suggesting the possibility of gaps in our understanding of their proteomic and genomic expression. A web-based pipeline for spectral networks analysis is available at http://proteomics.ucsd.edu/software.

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can be used to analyze complex “omics” data and to infer and optimize metabolic processes. Thereby, SMN models are suitable to capitalize on advances in high-throughput molecular and metabolic data generation. SMN models are starting to be applied to describe microbial interactions during wastewater treatment, in-situ bioremediation, microalgae blooms methanogenic fermentation, and bioplastic production. Despite their current challenges, we envisage that SMN models have future potential for the design and development of novel growth media, biochemical pathways and synthetic microbial associations.

Harnessing dark fermentative hydrogen from pretreated mixture of food waste and sewage sludge under sequencing batch mode

Food waste and sewage sludge are the most abundant and problematic organic wastes in any society. Mixture of these two wastes may provide appropriate substrate condition for dark fermentative biohydrogen production based on synergistic mutual benefits. This work evaluates continuous hydrogen production from the cosubstrate of food waste and sewage sludge to verify mechanisms of performance improvement in anaerobic sequencing batch reactors. Volatile solid concentration and mixing ratio of food waste and sludge were adjusted to 5 % and 80:20, respectively. Five different hydraulic retention times (HRT) of 36, 42, 48, 72, and 108 h were tested using anaerobic sequencing batch reactors to find out optimal operating condition. Results show that the best performance was achieved at HRT 72 h, where the hydrogen yield, the hydrogen production rate, and hydrogen content were 62.0 mL H2/g VS, 1.0 L H2/L/day, and ~50 %, respectively. Sufficient solid retention time (143 h) and proper loading rate (8.2 g COD/L/day as carbohydrate) at HRT 72h led to the enhanced performance with better hydrogen production showing appropriate n-butyrate/acetate (B/A) ratio of 2.6. Analytical result of terminal-restriction fragment length polymorphism revealed that specific peaks associated with Clostridium sp. and Bacillus sp. were strongly related to enhanced hydrogen production from the cosubstrate of food waste and sewage sludge.

Direct membrane-carbonation photobioreactor producing photoautotrophic biomass via carbon dioxide transfer and nutrient removal

An advanced-material photobioreactor, the direct membrane-carbonation photobioreactor (DMCPBR), was tested to investigate the impact of directly submerging a membrane carbonation (MC) module of hollow-fiber membranes inside the photobioreactor. Results demonstrate that the DMCPBR utilized over 90% of the supplied CO2 by matching the CO2 flux to the C demand of photoautotrophic biomass growth. The surface area of the submerged MC module was the key to control CO2 delivery and biomass productivity. Tracking the fate of supplied CO2 explained how the DMCPBR reduced loss of gaseous CO2 while matching the inorganic carbon (IC) demand to its supply. Accurate fate analysis required that the biomass-associated C include soluble microbial products as a sink for captured CO2. With the CO2 supply matched to the photosynthetic demand, light attenuation limited the rate microalgal photosynthesis. The DMCPBR presents an opportunity to improve CO2-deliver efficiency and make microalgae a more effective strategy for C-neutral resource recovery.

Relieving the fermentation inhibition enables high electron recovery from landfill leachate in a microbial electrolysis cell

The energy value of the organic matter in landfill leachate can be captured with a microbial electrolysis cell (MEC), which oxidizes organic compounds at an anode and generates H₂gas at a cathode.

Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity

Cyanobacteria have played a crucial role in the history of early earth and continue to be instrumental in shaping our planet, yet applications of cutting edge technology have not yet been widely used to explore cyanobacterial diversity. To provide adequate background, we briefly review current sequencing technologies and their innovative uses in genomics and metagenomics. Next, we focus on current cell capture technologies and the challenges of using them with cyanobacteria. We illustrate the utility in coupling breakthroughs in DNA amplification with cell capture platforms, with an example of microfluidic isolation and subsequent targeted amplicon sequencing from individual terrestrial thermophilic cyanobacteria. Single cells of thermophilic, unicellular Synechococcus sp. JA-2-3-B'a(2-13) (Syn OS-B') were sorted in a microfluidic device, lysed, and subjected to whole genome amplification by multiple displacement amplification. We amplified regions from specific CRISPR spacer arrays, which are known to be highly diverse, contain semi-palindromic repeats which form secondary structure, and can be difficult to amplify. Cell capture, lysis, and genome amplification on a microfluidic device have been optimized, setting a stage for further investigations of individual cyanobacterial cells isolated directly from natural populations.

Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone

Identifying specific gut microorganisms associated with chronic constipation may be useful for diagnostic and therapeutic purposes. The objective of this study was to evaluate whether or not the gut microbial community of constipated subjects had specific microbial signatures and to assess the effects of lubiprostone treatment on the gut microbial community. Stool diaries, breath H2 and CH4 levels, and stool samples were collected from ten healthy subjects and nine patients meeting the Rome III criteria for chronic functional constipation. Constipated subjects received lubiprostone for four weeks, during which stool diaries were maintained. Stool samples were evaluated for gut microbial communities using pyrosequencing and quantitative real-time PCR (qPCR) targeting 16S-rRNA gene, along with concentrations of short-chain fatty acids (SCFAs) using high-performance liquid chromatography. Prior to treatment, gut microbial profiles were similar between constipated subjects and healthy subjects, while iso-butyrate levels were significantly higher in constipated subjects compared with healthy subjects. Despite increases in stool frequency and improvements in consistency after lubiprostone treatment, gut microbial profiles and community diversity after treatment showed no significant change compared to before treatment. While we did not observe a significant difference in either breath methane or archaeal abundance between the stool samples of healthy and constipated subjects, we confirmed a strong correlation between archaeal abundance measured by qPCR and the amount of methane gas exhaled in the fasting breath. Butyrate levels, however, were significantly higher in the stool samples of constipated subjects after lubiprostone treatment, suggesting that lubiprostone treatment had an effect on the net accumulation of SCFAs in the gut. In conclusion, lubiprostone treatment improved constipation symptoms and increased levels of butyrate without substantial modification of the gut microbial structure.

Fate of Trace Metals in Anaerobic Digestion

A challenging, and largely uncharted, area of research in the field of anaerobic digestion science and technology is in understanding the roles of trace metals in enabling biogas production. This is a major knowledge gap and a multifaceted problem involving metal chemistry; physical interactions of metal and solids; microbiology; and technology optimization. Moreover, the fate of trace metals, and the chemical speciation and transport of trace metals in environments--often agricultural lands receiving discharge waters from anaerobic digestion processes--simultaneously represents challenges for environmental protection and opportunities to close process loops in anaerobic digestion.

Methods for understanding microbial community structures and functions in microbial fuel cells: a review

Microbial fuel cells (MFCs) employ microorganisms to recover electric energy from organic matter. However, fundamental knowledge of electrochemically active bacteria is still required to maximize MFCs power output for practical applications. This review presents microbiological and electrochemical techniques to help researchers choose the appropriate methods for the MFCs study. Pre-genomic and genomic techniques such as 16S rRNA based phylogeny and metagenomics have provided important information in the structure and genetic potential of electrode-colonizing microbial communities. Post-genomic techniques such as metatranscriptomics allow functional characterizations of electrode biofilm communities by quantifying gene expression levels. Isotope-assisted phylogenetic analysis can further link taxonomic information to microbial metabolisms. A combination of electrochemical, phylogenetic, metagenomic, and post-metagenomic techniques offers opportunities to a better understanding of the extracellular electron transfer process, which in turn can lead to process optimization for power output.

Substrate induced emergence of different active bacterial and archaeal assemblages during biomethane production

This study analyzed the composition of a methane-generating microbial community and the corresponding active members during the transformation of three target substrates (food waste, cellulose or xylan) by barcoded 454 pyrosequencing of the bacterial and archaeal 16S rRNA genes in the DNA and RNA. The number of operational taxonomic units at 97% similarity for bacteria and archaea ranged from 162-261 and 31-166, respectively. Principal coordinates analysis and Venn diagram revealed that there were significant differences in the microbial community structure between the active members transforming each substrate and the inoculum. The active bacterial populations detected were those required for the hydrolysis of the amended substrate. The active archaeal populations were methanogens but the ratio of Methanosarcinales and Methanomicrobiales varied between the cultures. Overall, results of this study showed that a subset of the populations became active and altered in relative abundance during methane production according to the amended substrate.

Do biological-based strategies hold promise to biofouling control in MBRs?

Biofouling in membrane bioreactors (MBRs) remains a primary challenge for their wider application, despite the growing acceptance of MBRs worldwide. Research studies on membrane fouling are extensive in the literature, with more than 200 publications on MBR fouling in the last 3 years; yet, improvements in practice on biofouling control and management have been remarkably slow. Commonly applied cleaning methods are only partially effective and membrane replacement often becomes frequent. The reason for the slow advancement in successful control of biofouling is largely attributed to the complex interactions of involved biological compounds and the lack of representative-for-practice experimental approaches to evaluate potential effective control strategies. Biofouling is driven by microorganisms and their associated extra-cellular polymeric substances (EPS) and microbial products. Microorganisms and their products convene together to form matrices that are commonly treated as a black box in conventional control approaches. Biological-based antifouling strategies seem to be a promising constituent of an effective integrated control approach since they target the essence of biofouling problems. However, biological-based strategies are in their developmental phase and several questions should be addressed to set a roadmap for translating existing and new information into sustainable and effective control techniques. This paper investigates membrane biofouling in MBRs from the microbiological perspective to evaluate the potential of biological-based strategies in offering viable control alternatives. Limitations of available control methods highlight the importance of an integrated anti-fouling approach including biological strategies. Successful development of these strategies requires detailed characterization of microorganisms and EPS through the proper selection of analytical tools and assembly of results. Existing microbiological/EPS studies reveal a number of implications as well as knowledge gaps, warranting future targeted research. Systematic and representative microbiological studies, complementary utilization of molecular and biofilm characterization tools, standardized experimental methods and validation of successful biological-based antifouling strategies for MBR applications are needed. Specifically, in addition, linking these studies to relevant operational conditions in MBRs is an essential step to ultimately develop a better understanding and more effective and directed control strategy for biofouling.

A photometric high-throughput method for identification of electrochemically active bacteria using a WO3 nanocluster probe

Electrochemically active bacteria (EAB) are ubiquitous in environment and have important application in the fields of biogeochemistry, environment, microbiology and bioenergy. However, rapid and sensitive methods for EAB identification and evaluation of their extracellular electron transfer ability are still lacking. Herein we report a novel photometric method for visual detection of EAB by using an electrochromic material, WO₃ nanoclusters, as the probe. This method allowed a rapid identification of EAB within 5 min and a quantitative evaluation of their extracellular electron transfer abilities. In addition, it was also successfully applied for isolation of EAB from environmental samples. Attributed to its rapidness, high reliability, easy operation and low cost, this method has high potential for practical implementation of EAB detection and investigations.

Relating MEC population dynamics to anode performance from DGGE and electrical data

The microbial electrolysis cell (MEC) is a promising system for H2 production, but little is known about the active microbial population in MEC systems. Therefore, the microbial community of five different MEC graphite felt anodes was analyzed using denaturing gradient gel electrophoresis (DGGE) profiling. The results showed that the bacterial population was very diverse and there were substantial differences between microorganisms in anolyte and anode samples. The archaeal population in the anolyte and at the anodes, and between the different MEC anodes, was very similar. SEM and FISH imaging showed that Archaea were mainly present in the spaces between the electrode fibers and Bacteria were present at the fiber surface, which suggested that Bacteria were the main microorganisms involved in MEC electrochemical activity. Redundancy analysis (RDA) and QR factorization-based estimation (QRE) were used to link the composition of the bacterial community to electrochemical performance of the MEC. The operational mode of the MECs and their consequent effects on current density and anode resistance on the populations were significant. The results showed that the community composition was most strongly correlated with current density. The DGGE band mostly correlated with current represented a Clostridium sticklandii strain, suggesting that this species had a major role in current from acetate generation at the MEC anodes. The combination of RDA and QRE seemed especially promising for obtaining an insight into the part of the microbial population actively involved in electrode interaction in the MEC.

Responses of Synechocystis sp. PCC 6803 to total dissolved solids in long-term continuous operation of a photobioreactor

This study evaluated how Synechocystis sp. PCC 6803 responds to high total dissolved solids (TDS) associated with eliminating nutrient limitation during long-term operation of a photobioreactor. The unique feature is that the TDS were not dominated by Na(+) and Cl(-), as in seawater, but by HCO(3)(-) and NO(3)(-) from nutrient delivery. The TDS-stress threshold was about 10 g/L. Whereas inorganic N and P limitations slowed the rate of inorganic C (C(i)) uptake in the light, TDS stress was manifested most strongly as a substantial increase of endogenous respiration rate at night. Relief from TDS stress was incomplete when lowered pH led to a HCO(3)(-) increase (560 mgC/L as a threshold). Impaired photosynthesis led to a cascade of reduced C(i)-uptake, pH decrease, HCO(3)(-) accumulation, and HCO(3)(-)-associated stress. Thus, long-term photobioreactor operation requires balancing the delivery rates of CO(2), N, P, and other TDS components to avoid general and C(i)-associated TDS stresses.

Flavins secreted by bacterial cells of Shewanella catalyze cathodic oxygen reduction

On Her Majesty's Secrete Service: Oxygen reduction is an important process for microbial fuel cells (MFCs) and microbiologically-influenced corrosion (MIC). We demonstrate that flavins secreted by anode-respiring Shewanella cells can catalyze cathodic oxygen reduction via adsorption on the cathode. The findings will provide new insight for developing methods to improve MFC performance and to prevent MIC.

Fatty acid profiling and molecular characterization of some freshwater microalgae from India with potential for biodiesel production

We determined the fatty acid compositions of six species of freshwater microalgae belonging to the Chlorophyta, which were isolated from freshwater bodies in Assam, India. All six microalgae -Desmodesmus sp. DRLMA7, Desmodesmus elegans DRLMA13, Scenedesmus sp. DRLMA5, Scenedesmus sp. DRLMA9 Chlorella sp. DRLMA3 and Chlorococcum macrostigmatum DRLMA12-showed similar fatty acid profiles 16:0, 16:4, 18:1, 18:2, and 18:3 as major components. We also compared fatty acid compositions during the late exponential and stationary growth phases of D. elegans DRLMA13 and Scenedesmus sp. DRLMA9 in BG11 medium. We observed enhanced percentages of total saturated and monounsaturated fatty acids with a concomitant decrease in polyunsaturated fatty acid content upon the prolonged cultivation of both microalgae. Distinct morphological features of microalgal isolates were determined by scanning electron microscopic (SEM) studies. An ornamented cell wall was found in D. elegans DRLMA13, which is characteristic of small spineless species of Desmodesmus. The isolated microalgae were further distinguished through analysis of internal transcribed spacer 2 (ITS2) secondary structures and compensatory base changes (CBCs). Analysis of CBCs showed the relatedness of Chlorella sp. DRLMA3 with other Chlorella-like organisms, but it does not belong to the clade comprising Chlorella sensu stricto, which includes Chlorella vulgaris. The CBC count between Scenedesmus sp. DRLMA9 and other species of Scenedesmus provides evidence that this isolate represents a new species.

Anaerobic digestion and co-digestion processes of vegetable and fruit residues: process and microbial ecology

This study evaluated the feasibility of methane production from fruit and vegetable waste (FVW) obtained from the central food distribution market in Mexico City using an anaerobic digestion (AD) process. Batch systems showed that pH control and nitrogen addition had significant effects on biogas production, methane yield, and volatile solids (VS) removal from the FVW (0.42 m(biogas)(3)/kg VS, 50%, and 80%, respectively). Co-digestion of the FVW with meat residues (MR) enhanced the process performance and was also evaluated in a 30 L AD system. When the system reached stable operation, its methane yield was 0.25 (m(3)/kg TS), and the removal of the organic matter measured as the total chemical demand (tCOD) was 65%. The microbial population (general Bacteria and Archaea) in the 30 L system was also determined and characterized and was closely correlated with its potential function in the AD system.

Roles of microorganisms other than Clostridium and Enterobacter in anaerobic fermentative biohydrogen production systems--a review

Anaerobic fermentative biohydrogen production, the conversion of organic substances especially from organic wastes to hydrogen gas, has become a viable and promising means of producing sustainable energy. Successful biological hydrogen production depends on the overall performance (results of interactions) of bacterial communities, i.e., mixed cultures in reactors. Mixed cultures might provide useful combinations of metabolic pathways for the processing of complex waste material ingredients, thereby supporting the more efficient decomposition and hydrogenation of biomass than pure bacteria species would. Therefore, understanding the relationships between variations in microbial composition and hydrogen production efficiency is the first step in constructing more efficient hydrogen-producing consortia, especially when complex and non-sterilized organic wastes are used as feeding substrates. In this review, we describe recent discoveries on bacterial community composition obtained from dark fermentation biohydrogen production systems, with emphasis on the possible roles of microorganisms that co-exist with common hydrogen producers.

Three-dimensional carbon nanotube-textile anode for high-performance microbial fuel cells

Microbial fuel cells (MFCs) harness the metabolism of microorganisms, converting chemical energy into electrical energy. Anode performance is an important factor limiting the power density of MFCs for practical application. Improving the anode design is thus important for enhancing the MFC performance, but only a little development has been reported. Here, we describe a biocompatible, highly conductive, two-scale porous anode fabricated from a carbon nanotube-textile (CNT-textile) composite for high-performance MFCs. The macroscale porous structure of the intertwined CNT-textile fibers creates an open 3D space for efficient substrate transport and internal colonization by a diverse microflora, resulting in a 10-fold-larger anolyte-biofilm-anode interfacial area than the projective surface area of the CNT-textile. The conformally coated microscale porous CNT layer displays strong interaction with the microbial biofilm, facilitating electron transfer from exoelectrogens to the CNT-textile anode. An MFC equipped with a CNT-textile anode has a 10-fold-lower charge-transfer resistance and achieves considerably better performance than one equipped with a traditional carbon cloth anode: the maximum current density is 157% higher, the maximum power density is 68% higher, and the energy recovery is 141% greater.

Integrating high-throughput pyrosequencing and quantitative real-time PCR to analyze complex microbial communities

New high-throughput technologies continue to emerge for studying complex microbial communities. In particular, massively parallel pyrosequencing enables very high numbers of sequences, providing a more complete view of community structures and a more accurate inference of the functions than has been possible just a few years ago. In parallel, quantitative real-time PCR (QPCR) allows quantitative monitoring of specific community members over time, space, or different environmental conditions. In this review, we discuss the principles of these two methods and their complementary applications in studying microbial ecology in bioenvironmental systems. We explain parallel sequencing of amplicon libraries and using bar codes to differentiate multiple samples in a pyrosequencing run. We also describe best procedures and chemistries for QPCR amplifications and address advantages of applying automation to increase accuracy. We provide three examples in which we used pyrosequencing and QPCR together to define and quantify members of microbial communities: in the human large intestine, in a methanogenic digester whose sludge was made more bioavailable by a high-voltage pretreatment, and on the biofilm anode of a microbial electrolytic cell. We highlight our key findings in these systems and how both methods were used in concert to achieve those findings. Finally, we supply detailed methods for generating PCR amplicon libraries for pyrosequencing, pyrosequencing data analysis, QPCR methodology, instrumentation, and automation.