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A Vista for Microbial Ecology and Environmental Biotechnology
Abstract
Microbial ecology and environmental biotechnology are blossoming fields that are taking advantage of profound advances in biology, materials, computing, and engineering. Although traditionally microbial ecology and environmental biotechnology have been distinct disciplines, their futures are intimately linked. Together, they offer much promise for helping society deal with some of its greatest challenges in environmental quality, sustainability, security, and human health.
... Microorganisms that drive the transformation of nutrients, play a vital role in environmental biotechnology (Rittmann et al., 2006). Nutrient elements, as the basis of synthesis of important polymers of life, are required for the growth of microorganisms. ...
... Since DIET can occur among certain types of syntrophic partners under specific conditions, microbial community structures and interaction patterns are considered to be crucial factors that determine the pathways of electron exchange. Numerous microorganisms form microbial communities with property of self-organization and self-sustainability (Rittmann et al., 2006). Disentangling the microbial community formation process is necessary to guide the regulation of the desired community structure. ...
... The microbial community structure and function in polluted environment has been out of balance. Understanding the ecological mechanisms of microbial community assembly is significant optimize the community structure in a contaminated environment (Rittmann et al., 2006). Carbon material can improve the effectiveness of bioremediation by increasing the uptake and accumulation of pollutants as well as prompting the degradation rate of contaminants by activating the ability of microorganisms to utilize contaminants (Wang et al., 2013;Zhao et al., 2018). ...
Understanding the underlying mechanism that drives the microbial community mediated by graphene derivative is crucial for achieving the enhancement of biological nitrogen removal by external stimulation. The main objectives of this study were to identify the bacterial community assembly mechanism via null model test and molecular ecological network analysis in the sediment culture system. Results showed graphene derivative increased biological nitrogen removal efficiency by 125%. The high electron transfer efficiency and denitrifying enzyme activities were achieved. Deterministic assembly is dominate (> 90%) in all the community assembly while the stochastic assembly process only existed in graphene derivative system (6.67%). The nitrogen removal was enhanced due to the intensification of the interaction on the microbial community between stochastic assembly and deterministic assembly. Keystone taxa in the graphene derivative systems, including Sulfuricella, Rhodobacter, and Comamonadaceae, drove the alteration of community structure relating to the nitrogen removal.
... The Environmental biotechnology started with wastewater treatment within the turn of the 19/20th century [1] and provided services for the removal of contaminants from wastewater and soil, to monitor pollutants and harmful materials within the environment and to recovery valuable products from waste [2]. In recent decades, it's offered many methods for environmental pollution and has become a technology for sustainable development. ...
... Indeed, biodegradation is the process by which organic substances are broken down into smaller compounds by living microbial organisms. Biodegradation provides useful strategies towash up many sorts of and xenobiotic pollutants like polycyclic hydrocarbon (PAH), organic metals, and halogenated or sulfur compounds [2][3]. The combination of genetics and process engineering, biodegradation and decomposition ISSN www.ijsrp.org ...
... The application of bioremediation methods, despite its frequent success, often leads to unexpected results due to the complex interactions taking place in the environment [18]. Hence, it is crucial to comprehend this complexity to fully understand how different factors might influence these processes in order to improve its management. ...
... The application of bioremediation technologies in situ is often challenged by unanticipated outcomes and impaired performance [18]. Differences in environmental parameters (e.g., pH and temperature), indigenous populations, and the complex interactions between their differences may lead to this uncontrolled behavior [34]. ...
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.
... Engineered microorganisms can offer a more cost-effective and secure substitute for conventional methods. structure, phenotypic potential, and function of genetically engineered organisms (GEO) interactions with the environment [9]. According to Eapen [10], Macek [11], Doty [12], and Panz[13], bioremediation utilising GEO is a relatively affordable, ecologically benign, and socially acceptable technology that may permanently eradicate waste. ...
Domestic and industrial pollution has been eliminated in the modern environment through physical and chemical means. However, these methods are pricy and harmful to the environment. The development of genetically modified microbes (GEMs) for bioremediation pollution abatement was prompted by the growing environmental contamination. Pollutants like oil spills, camphor, hexane, naphthalene, toluene, octane, and halo benzoates have been broken down using GEMs such bacteria, fungi, and algae. These genetically altered bacteria are quicker to adapt to different contaminants as co-metabolizers or substrates than wild strains, making them more effective than those. Engineered microorganisms can offer a more cost-effective and secure substitute for conventional methods.
... Transposable elements, conjugative plasmids and integrative and conjugative transposons all appear to aid in the transmission of genes that code for biodegradative activity. Both the plasmid-containing cells, specific growth rate and different concentrations of substrate had a massive effect on the rate coefficients, showing that the cells' energy to facilitate transference was restricted (Rittmann et al., 2006). Horizontal gene transfer of recombinant genes can be done swiftly using the same methods as before. ...
The book entitled Microbial Bioremediation: Sustainable Management of Environmental Contamination presents a set of microorganism-prompted technolo
gies for environmental hygiene. These technologies are based on the use of meta
bolic capabilities of microorganisms to remove contaminants from soils and waters. The concept of the book starts from the idea that through microbial remediation, a wide variety of polluting and toxic organic compounds can be bio-transformed until they become harmless. Microbial bioremediation can even degrade some organic compounds to their simplest forms, such as CH4 and CO2. The technologies dis
cussed under this theme can extract or immobilize environmental toxic substances and will be no longer available in toxic forms to living organisms. Furthermore, reducing the bioavailability of a toxic substance has been reconnoitred well, although it does not involve removing the substance from the environment. In the practice of “microbial bioremediation,” several concepts are used to reflect the bio
remediation process, depending on the type of action of microorganisms involved in the remediation process and bio-restoration of disturbed ecosystems.
We are enormously thankful to all the authors who have contributed to this book, and to the Springer team for their substantial teamwork and for printing this volume.
... Studies so far have not yet allowed for a definitive conclusion on their relationships. Filling this information gap is a very important task towards a complete understanding of microbiomes, and it directly relates to how human being can change the ecosystems surrounding us (Rittmann et al., 2006;McMahon et al., 2007). For instance, both positive and negative correlations between stochasticity and community functions have been reported. ...
... In order to ensure its application to practical systems, the ICPB system must continuously run around the clock with consistent efficiency, even under adverse environmental conditions (Rittmann et al., 2006). At present, investigations on the ICPB system put more effort into the components' amelioration, whereas our understanding of the system condition and mechanisms in a realistic environment remains limited. ...
The intimate coupling of photocatalysis and biodegradation (ICPB) possesses an enhanced ability of recalcitrant contaminant removal and energy generation, owing to the compact communication between biotic components and photocatalysts during the system operation. The photocatalysts in the ICPB system could dispose of noxious contaminants to relieve the external pressure on microorganisms which could realize the mineralization of the photocatalytic degradation products. However, due to the complex components in the composite system, the mechanism of the ICPB system has not been completely understood. Moreover, the variable environmental conditions would play a significant role in the ICPB system performance. The further development of the ICPB scheme requires clarification on how to reach an accurate understanding of the system condition during the practical application. This review starts by offering detailed information on the system construction and recent progress in the system components' amelioration. We then describe the potential influences of relevant environmental factors on the system performance, and the analytical strategies applicable for comprehending the critical processes during the system operation are further summarized. Finally, we put forward the research gaps in the current system and envision the system's prospective application. This review provides a valuable reference for future researches that are devoted to assessing the environmental disturbance and exploring the reaction mechanisms during the practical application of the ICPB system.
... Despite the ongoing controversy of the ''1% culturability paradigm,'' a majority of microorganisms in bioreactors, including specific functional species, may still be unculturable (Martiny, 2019(Martiny, , 2020Steen et al., 2019). The rapid development of sequencing technology in the last 20 years has revealed an enormous microbial diversity; this has emerged as a culture-independent method to explore the ecological mechanisms underlying bioreactor microbial communities, advancing the understanding of hidden microbial ecological systems underpinning reactor performance (Rittmann et al., 2006). ...
We investigated the short-term dynamics of microbial composition and function in bioreactors with inocula collected from full-scale and lab-based AD (anaerobic digestion) systems. The Bray-Curtis dissimilarity of both inocula was approximately 10% of the predicted KEGG pathway and 40% of the taxonomic composition, and yet resulted in a similar performance in methane production, implying the variation of community composition may be decoupled from performance. However, the significant correlation of VFAs with taxonomic variation suggested that the pathways of anaerobic digestion could be different due to the varying genus. The predicted function of the significantly varying genus was mostly related to fermentation, which strengthened the conclusion that most microbial variation occurred within the fermentative species and led to alternative routes to result in similar methane production in methanogenic bioreactors. This finding sheds a light on the understanding of AD community regulation, which depends on the aims to recover intermediates or methane.
... The typical procedure consists of biomass sampling and pretreatment, nucleic acid extraction, design of specific primers and polymerase chain reaction (PCR). When amplified nucleic acid is obtained, microbial community structure and phylogeny can be analyzed with various methods such as clone library and sequencing, pyrosequencing, denaturing gel gradient electrophoresis (DGGE), and terminal restriction fragment length polymorphism (T-RFLP) (Head et al. 1998;Forney et al. 2004;Rittmann et al. 2006). ...
Proper management and disposal of municipal solid waste (MSW) remains an unresolved global problem. One solution to handle existing and future MSW is to move away from modern landfills that focus on containment and move towards bioreactor landfills that promote MSW biodegradation and enhance methane (CH4) generation and its collection as an alternative energy source. Solid, liquid and gas phases of MSW coexist in different proportions within a landfill, and evolve with time due to concurring and coupled physical-biochemical-mechanical-hydraulic processes during MSW biodegradation. A fundamental understanding of the concurring processes is needed to design, monitor, and operate bioreactor landfills effectively and efficiently. Seven large-size (d=300 mm; h=600 mm) laboratory landfill simulators were developed to degrade unprocessed MSW of variable waste composition that is representative of the MSW in a mega-scale landfill. The simulators were operated and monitored for up to four years to assess the evolution of the physical, mechanical, and hydraulic properties of MSW, the evolution of the biochemical characteristics of generated leachate and biogas, and population dynamics of MSW-degrading microorganisms. The coupled processes were found to be systematic, correlated to each other, and dependent on initial waste composition. Testing of MSW in fresh and fully-degraded (retrieved from laboratory simulators) states was performed to assess the physical and mechanical properties of MSW using a unique 300-mm diameter simple shear apparatus. The shear strength and compressibility of MSW changed due to biodegradation and was a function of the initial waste composition and the biodegradation state. A relationship between the shear strength and shear-wave velocity of MSW was established for fresh and degraded MSW. Laboratory results on CH4 generation and settlement of MSW during biodegradation generated as part of this study were supplemented by an extensive database synthesized from the literature that includes laboratory results and field measurements from numerous landfills. The database was analyzed to quantify the influence of moisture content of waste, overburden pressure, landfill monitoring and control, and temperature on MSW degradation. Based on the findings of this study, recommendations to promote MSW biodegradation include enhancing biodegradation conditions, optimizing initial waste composition, and increasing biogas collection efficiency.
... But very often, remediation techniques fail in open ecosystems because of the difficulty to control and scale up key biodegradative processes from bench to full scale [4,5]. In order to succeed, a better understanding of the ecology of microbial communities inhabiting contaminated sites is needed, as well as of their interactions with the physicochemical environment [6]. However, studying the biology of environmental microbes is challenging, because most of them are recalcitrant to conventional cultivation. ...
Metagenomics, the culture-independent analysis of the collective genomes of microorganisms, is a powerful tool to access the genetic and metabolic diversity encoded in environmental microbes without the bias of cultivation. In particular, this technique is increasingly being applied to explore a great variety of microbial degradation pathways of pollutants, which remain to a large extent partly or totally uncharacterized. Based on a better knowledge of such pathways, more efficient customized strains/consortia could be designed for targeted use in bioremediation applications. Moreover, a better understanding of how microbial communities respond to environmental pollution is needed to predict the ability of contaminated sites to recover from pollution and to increase the chances of bioremediation strategies to succeed. We provide here an updated overview of past, present, and emerging applications of metagenomics to contaminated sites, discuss its limitations in the specific context of biodegradation, and report how such limitations are being overcome by methodological improvements.
... Studies so far have not yet allowed for a definitive conclusion on their relationships. Filling this information gap is a very important task towards a complete understanding of microbiomes, and it directly relates to how human being can change the ecosystems surrounding us (Rittmann et al., 2006;McMahon et al., 2007). For instance, both positive and negative correlations between stochasticity and community functions have been reported. ...
Ecological assembly processes, by influencing community composition, determine ecosystem functions of microbiomes. However, debate remains on how stochastic versus deterministic assembly processes influence ecosystem functions such as carbon and nutrient cycling. Towards a better understanding, we investigated three types of agroecosystems (the upland, paddy, and flooded) that represent a gradient of stochastic versus deterministic assembly processes. Carbon and nutrient cycling multifunctionality, characterized by nine enzymes associated with soil carbon, nitrogen, phosphorous and sulfur cycling, was evaluated and then associated with microbial assembly processes and co-occurrence patterns of vital ecological groups. Our results suggest that strong deterministic processes favour microorganisms with convergent functions (as in the upland agroecosystem), while stochasticity-dominated processes lead to divergent functions (as in the flooded agroecosystem). To benefit agroecosystems services, we speculate that it is critical for a system to maintain balance between its stochastic and deterministic assembly processes (as in the paddy agroecosystem). By doing so, the system can preserve a diverse array of functional traits and also allow for particular traits to flourish. To further confirm this speculation, it is necessary to develop a systematic knowledge beyond merely characterizing general patterns towards the associations among community assembly, composition, and ecosystem functions.
... To integrate new learning materials such as developed laboratory models in curriculum, an introductory environmental and nanotechnology course Introduction to Environmental Nanotechnology is being developed for senior undergraduates and graduate students. The topics cover concepts of nano/bio technologies (8)(9)(10) , their environmental applications and environmental risk assessment of nanomaterials. ...
... Microbial communities are an abundant natural resource that represents functional biological entities with diverse metabolic capacities. Various strategies have been used to optimize the management of microbial resources to tailor the needs of specific applications (Rittmann et al., 2006). Biological wastewater treatment systems are the most common large-scale examples of these strategies where microbes remove organic and inorganic pollutants, including ammonium (NH + 4 ), from wastewaters. ...
There is a lack of understanding of the interaction between anammox bacteria and the flanking microbial communities in both freshwater (non-saline) and marine (saline) ecosystems. Here, we present a comparative genome-based exploration of two different anammox bioreactors, through the analysis of 23 metagenome-assembled genomes (MAGs), 12 from freshwater anammox reactor (FWR), and 11 from marine anammox reactor (MWR). To understand the contribution of individual members to community functions, we applied the index of replication (iRep) to determine bacteria that are actively replicating. Using genomic content and iRep information, we provided a potential ecological role for the dominant members of the community based on the reactor operating conditions. In the non-saline system, anammox (Candidatus Brocadia sinica) and auxotrophic neighboring bacteria belonging to the phyla Ignavibacteriae and Chloroflexi might interact to reduce nitrate to nitrite for direct use by anammox bacteria. Whereas, in the saline reactor, anammox bacterium (Ca. Scalindua erythraensis) and flanking community belonging to phyla Planctomycetes (different than anammox bacteria)—which persistently growing in the system—may catabolize detritus and extracellular material and recycle nitrate to nitrite for direct use by anammox bacteria. Despite different microbial communities, there was functional redundancy in both ecosystems. These results signify the potential application of marine anammox bacteria for treating saline N-rich wastewaters.
... On progresse de plus en plus rapidement. Parallèlement à ce travail de description et de conceptualisation, il est désormais temps de mettre en mouvement ces connaissances dans un objectif de recherche appliquée(21)(22). Les perspectives ouvertes sont très larges, mais également très ambitieuses. ...
Dans le but d’évaluer la possibilité de mise en place une ingénierie écologique des processus microbiens de la digestion anaérobie dans les bioprocédés, différents leviers environnementaux ont été appliqués à des digesteurs de cellulose. Le premier levier étudié, de nature physico-chimique, était la température. Le deuxième faisait appel à une adaptation préalable d’une biomasse complexe par incubation avec des molécules simples avant mise en présence de cellulose. Le dernier consistait en la co-inoculation de diverses biomasses exogènes avec une boue anaérobie. Les conséquences des perturbations apportées par ces leviers sur les dynamiques métaboliques et écologiques de bioréacteurs anaérobies dégradant de la cellulose ont été évaluées. Différents indicateurs physico-chimiques ont été utilisés pour caractériser la dégradation de la cellulose (production de molécules intermédiaires, production de gaz, etc.). Les outils de la biologie moléculaire ont permis de caractériser les dynamiques microbiennes à l’échelle des communautés (par fingerprinting ARISA) ou des individus (par pyroséquençage de l’ADNr 16S). L’utilisation d’isotopes stables (cellulose marquée 13C), a permis de réaliser un traçage précis des flux de matières (intermédiaires de dégradation de la cellulose enrichis en 13C) et des microorganismes impliqués dans la chaîne de dégradation de la cellulose (groupes microbiens fonctionnels identifiés par la technique de "stable isotope probing"). Les expériences de changements de température ont montré l’influence importante de ce paramètre sur les communautés microbiennes, en particulier les archées. Elles ont mis en évidence le caractère asymétrique de l’effet de la température sur les communautés microbiennes et les conséquences irréversibles du passage par les conditions thermophiles. Ces propriétés ouvrent des perspectives intéressantes pour exploiter les chocs de température afin de modifier les propriétés de la biomasse. L’expérience de fonctionnalisation de la biomasse à l’aide de quatre molécules simples (acide propionique, acide butyrique, glucose et cellobiose) montre qu’un modelage des populations microbiennes par préadaptation est possible. Une fois en contact avec la cellulose, les biomasses fonctionnalisées génèrent des schémas de dégradation et des structures de communautés qui se répartissent de manière inattendue en deux catégories seulement. Ce résultat suggère qu’il est possible d’orienter les états d’équilibre d’une communauté microbienne complexe par préadaptation fonctionnelle. Enfin, des expériences de co-inoculation ont mis en avant la difficulté d’exploiter directement les propriétés enzymatiques de flores cellulolytiques performantes mais également les possibilités de modifier les équilibres de diversité au sein de la biomasse du bioprocédé. Ces expériences suggèrent qu’un paramètre tel que la diversité de la communauté d’un bioprocédé pourrait être manipulé par bioaugmentation. Ce travail démontre que nous disposons d’ores et déjà d’un certain nombre d’outils pour élaborer une ingénierie écologique des bioprocédés à travers une nouvelle démarche de gestion qui se place à l’échelle de l’écosystème microbien et des services associés.
... Advancement in field of biotechnology has led to introduction of new branch known as molecular microbial ecology. The genome dependent tools have led to discovery of new micro-organisms with new metabolic tendencies (Rittmann et al. 2006(Rittmann et al. , 2008. Different biotechnological approaches are involved in treating and disposal of wastewater in collaboration with environmental engineering. ...
The demand for freshwater is very high in the coastal regions due to the high population density in coastal areas. To meet this demand for freshwater, the coastal aquifers are often heavily pumped without any regulation, resulting in saltwater intrusion. Therefore, the biggest challenge in the management of coastal aquifer is to meet the demand for freshwater by pumping the coastal aquifer without causing saltwater intrusion. In this study, a brief overview of various methods for identification, prediction, and management of saltwater intrusion is presented. Detection of saltwater intrusion is largely hindered due to insufficient spatiotemporal monitoring because of budgetary constraints. Application, merits, and demerits of the newer cost-effective techniques as well as conventional techniques for identifying saltwater intrusion are discussed in this chapter. The application of various prediction models and their computational difficulties is also presented in this study. Finally, advanced techniques for identification and sustainable management practice in saltwater intrusion are discussed. Though significant progress has been made in the recent past in the management of coastal aquifers, they still show gaps in addressing real-life scenarios. An attempt has been made to highlight the suitability of a developed methodology and their respective limitations.
... Environmental biotechnology is one of the most important methods for the remediation of various polluted environments (Rittmann et al., 2006;Liu et al., 2018), for instance wastewater treatment. However, most natural microorganisms can only grow in environments with low concentrations of pollutants and usually transform pollutants with low efficiency. ...
Acclimation is the main method to enhance the productivity of microorganisms in environmental biotechnology, but it remains uncertain how microorganisms acquire resistance to high concentrations of pollutants during long-term acclimation. Shewanella oneidensis MR-1 was acclimated for 120 days with increasing hexavalent chromium (Cr(VI)) concentrations from 10 to 190 mg/L. The bacterium was able to survive from the highly toxic Cr(VI) environment due to its enhanced capability to reduce Cr(VI) and the increased cell membrane surface. We sequenced 19 complete genomes from 7 populations of MR-1, including the ancestral strain, the evolved strains in Cr(VI) environment on days 40, 80 and 120 and their corresponding controls. A total of 27, 49 and 90 single nucleotide polymorphisms were found in the Cr(VI)-evolved populations on days 40, 80 and 120, respectively. Nonsynonymous substitutions were clustered according to gene functions, and the gene mutations related to integral components of the membrane, including efflux pumps and transporters, were the key determinants of chromate resistance. In addition, MR-1 strengthened the detoxification of Cr(VI) through gene variations involved in adenosine triphosphate binding, electron carrier activity, signal transduction and DNA repair. Our results provide an in-depth analysis of how Cr(VI) resistance of S. oneidensis MR-1 is improved by acclimation, as well as a genetic understanding of the impact of long-term exposure of microorganisms to pollution.
... Biological water resource recovery relies upon complex selfassembled microbial communities to purify wastewater. These systems must be reliable and robust in order to protect the environment and public health (Rittmann et al., 2006). Effective monitoring is needed because process upsets at water resource recovery facilities (WRRFs) can often be attributed to a change in the relative abundance of a subpopulation of microorganisms (Graham and Smith, 2004). ...
The use of molecular probe technology is demonstrated for routine identification and tracking of cultured and uncultured microorganisms in an activated sludge bioreactor treating domestic wastewater. A key advantage of molecular probe technology is that it can interrogate hundreds of microbial species of interest in a single measurement. In environmental niches where a single genus (such as Competibacteraceae) dominates, it can be difficult and expensive to identify microorganisms that are present at low relative abundance. With molecular probe technology, it is straightforward.
Members of the Competibacteraceae family, none of which have been grown in pure culture, are abundant in an activated sludge system in the San Francisco Bay Area, California, USA. Molecular probe ensembles with and without Competibacteraceae probes were constructed. Whereas the probe ensemble with Competibacteraceae probes identified a total of ten bacteria, the molecular probe ensemble without Competibacteraceae probes identified 29 bacteria, including many at low relative abundance and including some species of public health significance.
... Although PCWDE have been characterized from plants (Johansson et al. 2002;Suzuki et al. 2002) and animals (Evangelista et al. 2015;Watanabe and Tokuda 2001;Pauchet et al. 2010), microorganisms represent the main s o u r c e f o r e n z y m e d i s c o v e r y. I n t h i s c o n t e x t , metatranscriptomic studies on complex unculturable microbial communities have greatly enhanced the pace of identification of enzymes from underexplored and uncultivable microorganisms (Castillo et al. 2013;Rittmann et al. 2006;Curtis et al. 2003;Duan and Feng 2010). For these reasons, we have conducted metatranscriptomic studies of a microbial consortium, which was grown in a nutrient-limited medium enriched with sugarcane bagasse, to selectively favor microorganisms capable of degrading PCW (Mello et al. 2016;Evangelista et al. 2018). ...
Biotechnologies that aim to produce renewable fuels, chemicals, and bioproducts from residual ligno(hemi)cellulosic biomass mostly rely on enzymatic depolymerization of plant cell walls (PCW). This process requires an arsenal of diverse enzymes, including xylanases, which synergistically act on the hemicellulose, reducing the long and complex xylan chains to oligomers and simple sugars. Thus, xylanases play a crucial role in PCW depolymerization. Until recently, the largest xylanase family, glycoside hydrolase family 11 (GH11) has been exclusively represented by endo-catalytic β-1,4- and β-1,3-xylanases. Analysis of a metatranscriptome library from a microbial lignocellulose community resulted in the identification of an unusual exo-acting GH11 β-1,4-xylanase (MetXyn11). Detailed characterization has been performed on recombinant MetXyn11 including determination of its low-resolution small angle Xray scattering (SAXS) molecular envelope in solution. Our results reveal that MetXyn11 is a monomeric globular enzyme that liberates xylobiose from heteroxylans as the only product. MetXyn11 has an optimal activity in a pH range from 6 to 9 and an optimal temperature of 50 oC. The enzyme maintained above 65% of its original activity in the pH range 5 to 6 after being incubated for 72 h at 50 oC. Addition of the enzyme to a commercial enzymatic cocktail (CelicCtec3) promoted a significant increase of enzymatic hydrolysis yields of hydrothermally pretreated sugarcane bagasse (16% after 24 h of hydrolysis).
... Also, as was stated by Jousset et al. (2011), resilience (the ability of a community to quickly recover after a perturbation), provides its members with an additional biotechnological feature. In this sense, Rittmann et al. (2006) suggested that, for fullscale biotechnological environmental-related processes, the focus should be put on microbial communities rather than on a "superbug" for the solution of different problems. ...
Hydrocarbon contamination in soils from extremely cold areas, such as those from Antarctica, requires the development of specific remediation strategies for cleaning up anthropogenic pollution. Previous reports evidenced that after on-site biostimulation process of gasoil-contaminated Antarctic soils, 20% of the initial hydrocarbons remained undegraded (mainly C11–C14 n-alkanes). In the present work, these n-alkanes were added as sole carbon and energy source to enrichment cultures inoculated with the previously treated soil (biostimulation) as microorganism’s source to investigate changes occurring in the bacterial community structure. Three subcultures (8, 16, and 24 days) were performed from each enrichment culture. Changes in bacterial communities among different cultures and its subcultures were evidenced by Denaturing Gradient Gel Electrophoresis (DGGE). Results showed that even differences of one C in the alkane chain-length led to different community structures that evolved divergently from the original one. Clusters analysis showed that while samples grouped mainly by culture time, substrate-dependent differences were also evident. Isolation of biological tools for bioremediation from the cultures showed that Pseudomonadaceae members were omnipresent, whereas Rhodococcus spp. were obtained in cultures with the longest chain-length substrates. Results provided evidence about the presence of certain substrate preference of soil bacteria (even when substrates differed only in one C-atom of their chain-length), leading to different community structures. A collection of psychrotolerant hydrocarbon degrading/tolerant strains was obtained, representing a valuable tool for the design of a bioaugmentation strategy as a second, more specific stage, targeting the remnant hydrocarbons after a first bioremediation process involving biostimulation.
... However, deterministic and stochastic processes were also found to be jointly responsible for shaping microbial community assembly in diverse environments (27). Previous studies provided a theoretical foundation for the optimization of WWTPs by investigating the rules underlying the assembly of AS microbial communities (7,44). The structures of AS microbial communities were recently shown to be mainly regulated by environmental or operational variables (e.g., temperature, dissolved oxygen (DO), chemical oxygen demand (COD), and nutrients) (12,24,35,54), suggesting that the dynamics of the AS microbial population is strongly controlled by deterministic factors (1,23,60). ...
Limited information is currently available on the assembly processes (deterministic vs. stochastic) shaping the compositions of key microbial communities in activated sludge (AS). The relative importance of deterministic and stochastic processes for key bacterial and archaeal assemblages (i.e., core-satellite and habitat generalist-specialist) in AS from 13 wastewater treatment plants in China was investigated using 16S rDNA amplicon sequencing. The results obtained indicated 1,388 and 369 core operational taxonomic units (OTUs), 1,038 and 1,683 satellite OTUs, 255 and 48 habitat generalist OTUs, and 192 and 111 habitat specialist OTUs for Bacteria and Archaea, respectively. The proportions of shared OTUs between core and habitat specialist communities were similar to or higher than those between core and habitat generalist communities, suggesting a stronger inter-linkage between the former two groups. Deterministic processes, indicated by abundance-based β-null models, were responsible for shaping core communities, in which NH4-N, OrgC/OrgN, Cr, and Ni were the main controlling factors. In contrast, satellite communities were predominantly influenced by stochastic processes. Moreover, we found that deterministic and stochastic processes were mainly responsible for shaping the assembly of habitat specialists and generalists, respectively. However, the influence of deterministic factors on habitat specialists remains unclear. The present study provides novel insights into the assembly mechanisms of AS microbial communities.
... The process of organic degradation is very complex. With regard to biological treatment, the degradation process is achieved by the metabolism of the microorganism, which can be divided into catabolism and anabolism processes (Claudia and Josef, 2005;Rittmann et al., 2006). In other words, the total biodegraded COD (COD biode ) consists of the catabolism part (COD cata ) and the anabolism part (COD ana ), as shown in Equation (3). ...
... Therefore, these microbial consortia have the attractive potential to accomplish complex tasks more efficiently than a single wild-type or engineered microbial strain. Past applications include applying communities to aid in waste decomposition, fuel cell development, and the creation of biosensors [1]. In the field of metabolic engineering, microbial communities have now been engineered capable of enhancing product yield or improving process stability by partitioning catalytic functions among community members [2][3][4][5][6][7][8]. ...
Author summary
Many basic characteristics underlying the establishment of cooperative growth in bacterial communities have not been studied in detail. The presented work sought to understand the adaptation of syntrophic communities by first employing a new computational method to generate a comprehensive catalog of E. coli auxotrophic mutants. Many of the knockouts in the catalog had the predicted effect of disabling a major biosynthetic process. As a result, these strains were predicted to be capable of growing when supplemented with many different individual metabolites (i.e., a non-specific auxotroph), but the strains would require a high amount of metabolic cooperation to grow in community. Three such non-specific auxotroph mutants from this catalog were co-cultured with a proven auxotrophic partner in vivo and evolved via adaptive laboratory evolution. In order to successfully grow, each strain in co-culture had to evolve under a pressure to grow cooperatively in its new niche. The non-specific auxotrophs further had to adapt to significant homeostatic changes in cell’s metabolic state caused by knockouts in metabolic genes. The genomes of the successfully growing communities were sequenced, thus providing unique insights into the genetic changes accompanying the formation and optimization of the viable communities. A computational model was further developed to predict how finite protein availability, a fundamental constraint on cell metabolism, could impact the composition of the community (i.e., the relative abundances of each community member).
... But very often, remediation techniques fail in open ecosystems because of the difficulty to control and scale up key biodegradative processes from bench to full scale [4,5]. In order to succeed, a better understanding of the ecology of microbial communities inhabiting contaminated sites is needed, as well as of their interactions with the physicochemical environment [6]. However, studying the biology of environmental microbes is challenging, because most of them are recalcitrant to conventional cultivation. ...
... function (i.e., which ones among those biocatalytic capabilities are realized?) and interactions with the environment ( Rittmann et al., 2006). As 90 to 99% of microbes living in natural environments are recalcitrant to conventional cultivation, the biggest boom in microbial ecology research undoubtedly came in the 1990s from the application of culture-independent molecular tools to study the diversity and dynamics of microbial communities in fine detail. ...
... 'why are they there?' and more critically 'who is doing what?', and 'what are the interrelationships among them, and between them and their environment?' (Rittmann et al., 2006). ...
Despite the long history of water research, understanding how the drinking water microbiome is shaped at the user end is rather challenging owing to the complexity in community assembly, water matrices, physical structures, and chemical gradients from source to tap. The application of molecular tools that primarily base on the use of rRNA gene sequences has substantially expanded our view of the drinking water microbiome. In this review, we critically evaluate currently available cultivation-independent tools for monitoring the drinking water microbiome and summarize the ecological patterns we have observed so far on the longitudinal and temporal dynamics, geographical distributions, and structural and functional characteristics of the drinking water microbiome (including those in recycled water systems). Studies on four full-scale systems in the United States and Europe further exemplify the application of ecological theory into drinking water microbiome studies. Finally, we discuss how meta-omics are able to provide new perspectives on microbial function and interspecies relationship within the drinking water ecosystem. This review promotes an integral understanding of the drinking water microbiome and the transformation of drinking water microbiology from a descriptive discipline to an ecology-driven science that attempts to elucidate mechanisms for predicting and shaping the microbiome at the user end.
... Microorganisms, regulating all major biogeochemical cycles, serve essential roles in environmental biotechnology. 1,2 With the attempts to link microbial communities with environmental processes, researchers believe that understanding the ecological mechanisms of community assembly controlling community diversity and its relationships to community functions becomes a very important task for the application of microbial biotechnology. 3,4 Knowledge about the process and factors controlling community assembly is critical to our understanding of the patterns of species composition and diversity. ...
Community assembly process (determinism vs. stochasticity) determines the composition and diversity of microbial community, and then shapes its functions. Understanding this complex process and its relationship to the community functions becomes a very important task for the applications of microbial biotechnology. In this study, we applied microbial electrolysis cells (MECs) with moderate species numbers and easily tractable functions as a model ecosystem, and constructed a series of biofilm communities with gradient biodiversity to examine the roles of community assembly in determining microbial community structure and functions. After stable biofilms formed, the best MEC reactor performances (e.g., gas productivity, total energy efficiency) were achieved in the group which biofilms had the second highest α-diversity, and biofilms with even lower diversity showed declining performance. Null model analyses indicated that both deterministic and stochastic assembly played roles in the formation of biofilm communities. When deterministic assembly dominates this formation, the higher diversity of biofilm community would generally show better reactor performance. However, when the stochasticity dominates the assembly process, the bioreactor performance would decline. This study provides novel evidence that the assembly mechanism could be one of the key processes to shift the functions, and proposes an important guidance for selecting the most efficient microorganisms for environmental biotechnologies.
... Several genes have been studied for their beneficial effects of being introduced into rhizobacteria and plants to improve biodegradation and bioaccumulation of persistent toxic metal elements in contaminated soils. Knowledge of the physicochemical properties of genetically engineered bacteria such as their phenotypic, metabolic, and symbiotic potential, as well as their interaction with the environment, makes it possible to better predict the effectiveness of bioremediation (Rittmann et al. 2006;Azad et al. 2014). Several previous studies have highlighted the development of transgenic technologies and its applications in bioremediation under complex environmental conditions (Ezezika et Singer 2010;Singh et al. 2011;Delgadillo et al. 2015). ...
Leguminous plants play a vital role in agriculture, economy, and even food security for the world’s population. Indeed, they are considered as a major source of protein for human food worldwide, providing 22% protein, 32% fat, and 7% carbohydrates. They provide a bulk of soil organic matter (SOM) in agricultural soils and have a crucial role in the soil for long-term sustainability. This is due to their significant role in improving soil fertility and ability to form Rhizobium-legume symbiosis enabling atmospheric nitrogen (N) fixation. Recently, Rhizobium-legume symbioses have attracted attention for their biochemical and ecological capacity to degrade and remove organic pollutants. They are also known for their resistance to heavy metal which make them efficient tools for rehabilitating contaminated soils. However, high heavy metal concentrations in soil may have an adverse effect on both Rhizobium and its host plant and also on their symbiotic properties. In fact, the repartition of heavy metals in soil is widespread, with an annual global heavy metal release estimated at 22.10⁻³ Tg of Cd, 939.10⁻³ Tg of Cu, 783.10⁻³ Tg of Pb, and 1.35 Tg of Zn. Moreover, consumption of agri-foods grown in heavy metal-polluted soils may have serious implications on human health. Recent data indicate that exposure to low levels of some heavy metals such as cadmium can have adverse health effects, mainly in the form of kidney damage, but also bone and fracture effects.
... These microbes can degrade a variety of chemicals to harmless products and can help in cycling the nitrogen, phosphorus and other elements. This particular nature of some microorganisms is being exploited by the industry as one of the most important application of biotechnology in industry (Rittmann, 2006;Rittmann et al., 2006). One of the primary criteria for biological treatment is that the wastewater stream should have more amount of such compounds that can be degraded to stable compounds like CO, CO 2 , NH 3 , CH 4 , H 2 S etc (Cheremsinoff, 1996;Dun et al., 2003). ...
... It is well established that microbe-based successful bioremediation strategies greatly depend on the understanding of the geochemical character of the contaminated sites along with the microbial communities involved in key physiological processes. As per the microbial communities are concerned, it showed demand on detail investigations to characterized its structure, metabolic potential, function, and interaction with inhabitant environments (Rittmann et al. 2006). Microorganisms in the terrestrial subsurface are responsible to mitigation of contaminants (Lloyd and Renshaw 2005;Gadd 2010;Dhal et al. 2011;Green et al. 2012). ...
Discharge of uranium (U) tailings and contaminant effluents from uranium ore extraction sites creates huge burdens of anthropogenic radioactivity and greatly alters the ecosystem. Remediating the environment from these contaminations thus becomes a huge responsibility of the industry. Microbe-based bioremediation has emerged as a potential alternative to hazardous mine waste management as well as removal of toxic contaminants efficiently from the environment. In order to formulate the bioremediation strategies effectively, it is essential to understand the inhabitant microbial community structure of mine sites and their metabolic role as related to those sites. In addition, deciphering microbial communities also helps us to understand the responsible biogeochemical cycling and food web dynamics of such sites. Advancement in different techniques that includes high-throughput DNA sequencing and different “omic” tools can provide details of microbial communities and their metabolic activity in contaminated environments. The present chapter will describe both culturable and unculturable microbial diversity, dynamics within the uranium tailing pond, and radionuclide-contaminated environment and their interaction with other heavy metals including uranium.
... But very often, remediation techniques fail because of the difficulty to control and expand key biodegradative processes from bench to full scale (Fantroussi and Agathos 2005;Paerl and Steppe 2003). To get better results, a better understanding of the ecology of microbial communities inhabiting contaminated sites is needed, as well as of their interactions with the environment (Rittmann et al. 2006). But, the complete study of the microbial communities of the environment is challenging as most of them are recalcitrant to conventional cultivation (Stewart 2012). ...
Heavy metal pollution, cleaning and recycling are a major environmental issue. In particular, there is a need for efficient techniques to treat wastewaters. Conventional technologies to treat industrial waters are limited by stringent health policies and emerging contaminants. Fungi-based nanotechnology is rapidly emerging as an effective technology to treat industrial wastewaters. This chapter reviews the recent developments in fungal biosorption, biological synthesis of nanoparticles using fungi, and the application of fungi-based nanosorbents for heavy metals removal.
... PCWDE have been extensively studied from a wide diversity of microorganisms, plants and animals [5][6][7]. Since only 0.1-1% of the microbes are cultivable under laboratory conditions in pure culture, metagenomics approaches, relying on next-generation sequencing, have greatly enhanced the bioprospection of novel interesting genes that are hidden in the unexplored non-cultivable microorganisms [8][9][10][11]. In order to access a large number of novel PCWDE, we performed metatranscriptomic studies of a sugarcane bagasse compost-derived consortia [12]. By using nutrient-limited medium enriched with sugarcane bagasse, the microbial consortia was selectively pressed in favor of microorganisms with capacity of degrading plant biomass [12]. ...
Environmental issues are promoting the development of innovative technologies for the production of renewable energy and "green products" from plant biomass residues. These technologies rely on the conversion of the plant cell wall (PCW) polysaccharides into simple sugars, which involve synergistic activities of different PCW degrading enzymes, including xylanases; these are widely applied in food and feed sectors, paper and textile industries, among others. We cloned, expressed and biochemically characterized a novel xylanase (Xyn10) from the GH10 identified in a metatranscriptome of compost-derived microbial consortia and determined its low-resolution SAXS molecular envelope in solution. Our results reveal that Xyn10 is a monomeric flexible globular enzyme, with high stability with a broad pH range from 4 to 10 and optimal activity conditions at pH 7 and 40 °C. Only 10% of activity loss was observed after the enzyme was incubated for 30 h at 40 °C with a pH ranging from 5 to 10. Moreover, Xyn10 maintained 100% of its initial activity after incubation for 120 h at 40 °C and 51% after incubation for 24 h at 50 °C (pH = 7.0). Xyn10 shows endocatalytic activity towards xylan and arabinoxylan, liberating xylose, xylobiose, 1,2-α-D-methylglucuronic acid decorated xylotriose, and 1,3-α-L-arabinofuranose decorated xylobiose and xylotriose oligosaccharides.
The design of biomass beds and feeding conditions is crucial for an optimal loading, microbial selection, and biological nutrient removal (BNR) in granular sludge processes. Polyphosphate- (PAOs) and glycogen-accumulating organisms (GAOs) compete for organic substrates during anaerobic phases of sequencing batch reactors (SBRs). System analysis and mathematical modeling was engaged to elucidate the hydraulic transport pattern during the up-flow feeding of wastewater in granular sludge beds and the impact of environmental conditions (pH, temperature) on PAO/GAO selection. Tracer experiments across the granular sludge column displayed a plug-flow regime with dispersion under both rapid (9 m h−1) and slow (0.9 m h−1) up-flow feedings. Fill-and-draw phases can be implemented in SBRs to feed the influent at foot and extract the treated effluent at the top. Metabolic simulations disclosed the effects of feeding duration, pH, and temperature on PAO/GAO competition for the uptake of volatile fatty acids (VFAs) under anaerobic slow feeding. Feeding time should be set in function of conversions of intracellular storage polymers that do not move with the liquid phase. The anaerobic metabolism of PAOs relies on both polyphosphate and glycogen as energy and reducing equivalents to store VFAs as poly-β-hydroxyalkanoates. PAOs withstand a feed period twice as long as GAOs in which only glycogen serves as pool of electrons and energy. Applying alkaline conditions (pH 7.25–8.0) by, e.g., dosing lime in the feed selects for PAOs independent of temperature (10–30 °C). Temperature determines the bed height necessary for optimal contact between wastewater and biomass in a full anaerobic selector for PAOs, and BNR. Almost twice higher beds are needed at 10 °C than at 20 °C for a complete anaerobic uptake of VFAs. This hydraulic-metabolic model sustains the design of bed geometries and feeding conditions to manage the microbial resource in granular sludge.
During the last century, large scale production of halogenated organic compounds and heavy
metals, specifically by industrial processes, and the inappropriate management of those products caused
a wide spreading of a variety of hazardous contaminants into the environment including a massive
contamination of the groundwater. Their presence and persistence have significantly influenced human
health and the environment. Recently, many technologies have been employed in order to reduce their
impacts. However, the majority of those technologies did not achieve the target, because of their high cost
and low efficacy in the reduction of contaminants. Nevertheless, a new technology of synergetic
interactions of (nZVI) zero-valent iron nanoparticles with two types of anaerobic bacteria; the
organohalide respiring bacteria (OHRB) and sulfate-reducing bacteria (SRB), have been investigated as
a promising technology for in-situ groundwater remediation. This powerful technique was successfully
utilized for the reduction of pollutants and converted to environmentally benign forms. This article
reviews and emphasizes the coupling effect of (nZVI-OHRB) and (nZVI-SRB) on the remediation process
of contaminated sites, in addition to a detailed illustration of the mechanism of the integration of (nZVIOHRB) and (nZVI-SRBs), and discussion of the influencing factors on the integrated system. Actually,
the technology presented here, though proven successfully, needs more case studies to better
understanding of the interactions between microorganisms and nZVI, as well as with the surrounding
environment for a better efficacy and finding the best solutions.
Identification and classification are now largely based on sequence analyses of ribosomal RNA (rRNA) or the rDNA encoding it, as well as genes of universally distributed enzymes, since this leads to phylogenetically more correct taxonomic groupings than traditional methods and since even very distant relationships can be analysed. In the following, therefore, the principles behind the most important molecular genetic methods for the identification and classification of isolated bacteria and for the characterization of microbial communities will be briefly presented. Structural and functional analyses with molecular biological approaches are todays methods to characterize a microbial population in Nature. These include basic molecular genetic methods for classification and identification of pure cultures as well as for community characterization. Metagenomics has been used to characterize a community of an acid mine drainage system, the Sargasso Sea environment or a global sampling expedition of the Pacific Ocean.
In the past few decades, environmental pollution has become a serious threat, affecting biodiversity, public health and communities all over the world. Currently, microbial potential is linked to the removal of contaminants from the environment. Bioremediation using genetically engineered microbes as novel, environmentally friendly more effective and less expensive method to remove pollutants from the contaminated sites. With a combination of genetically modified organisms and biological remediation, the effectiveness of the contaminated sites can be improved. This chapter comprised of new genetic approaches to study and improve these microorganisms. The application of GEMs in bioremediation is covered in depth, along with the creation of recombinant strains with desirable characteristics via route design and enzyme specificity alterations.
Microorganisms and their natural products are major drivers of ecological processes and industrial applications. Microbial bioprospecting has been critical for the advancement in various fields such as pharmaceuticals, sustainable industries, food security and bioremediation. Next generation sequencing has been paramount in the exploration of diverse environmental microbiomes. It presents a culture-independent approach to investigating hitherto uncultured taxa, resulting in the creation of massive sequence databases, which are available in the public domain. Genome mining searches available (meta)genomic data for target biosynthetic genes, and combined with the large-scale public data, this in-silico bioprospecting method presents an efficient and extensive way to uncover microbial bioproducts. Bioinformatic tools have progressed to a stage where we can recover genomes from the environment; these metagenome-assembled genomes present a way to understand the metabolic capacity of microorganisms in a physiological and ecological context. Environmental sampling been extensive across various ecological settings, including microbiomes with unique physicochemical properties that could influence the discovery of novel functions and metabolic pathways. Although in-silico methods cannot completely substitute in-vitro studies, the contextual information it provides is invaluable for understanding the ecological and taxonomic distribution of microbial genotypes and to form effective strategies for future microbial bioprospecting efforts.
BioremediationBioremediation may be defined as the mechanism by which a biological agent (e.g., microbesMicrobes, fungiFungi, plants, and enzymesEnzyme) is used to minimise soilSoil, groundwaterGroundwater, and air contaminant mass and toxicityToxicity. Bioremediation aims at reducing contamination and targeting the amounts of pollutants in water and/or soil by either biodegradation (of organic matter) or biotransformation (of metalsMetals). The monitoringMonitoring tests may provide necessary details on the bioremediationBioremediation process and usually include the use of analytical techniques (microbiological, biochemical or molecular) to determine, under certain situations, the status and effectiveness of bioremediation. By considering several micro-organisms with diverse genomes, expressed transcripts and proteins, bioremediation has become able to take advantage of approaches powered by genomics to observe, map and evaluate its path. Owing to the lack of sensitive methods of identification, the classification of microbial species poses restrictions. Conventional microbiological approaches, such as isolation of pure colonies and further study of their physiological and biochemical properties, are not always well suited for studies of microbial communities and their behaviour. In particular, more than 99% of microbial population in soils could not be segregated due to a lack of awareness of their physiological needs. Molecular techniques were thus created to compensate for the disadvantages found in conventional methods of culture. Molecular techniques based on 16S rRNARRNA, RTPCR, and real time PCR polymerase chain reaction (PCR), microarray, fingerprinting, and metaproteomicsMetaproteomics have become standard instruments for detecting and quantifying microorganisms previously added to soils. Similarly, other less traditional approaches such as FISHFISH(fluorescent in situIn situ hybridization), DGGE (denaturing gradient gel electrophoresis), TGGE (temperature gradient gel electrophoresis) and metagenomicsMetagenomics had been studied and applied to research and better understand the microbial degradation of polycyclic aromatic hydrocarbonsPolycyclic aromatic hydrocarbons(PAHsPAHs). The new genomic and metagenomic methodologies are intended to improve the exploration of new catabolic practises and to provide, from a sustainable development perspective, statistical and reliable reporting for the maintenance and clean-up of contaminated areas and wastes.
Microorganisms are deeply embedded in nearly every aspect of human activity and have significantly shaped the trajectory of mankind’s history. The important roles of microorganisms warrant the significant need for their rapid and sensitive detection. In this chapter, recent developments of a number of biosynthetic approaches for the detection of microorganisms are introduced. Because genetic information for microbes is stored in the nucleotide sequences that are usually species-specific, most recently developed methods for the identification and quantification of microbes target DNA or RNA sequences. The strategies covered here for nucleic acid detection include conventional quantitative polymerase chain reaction, various thermal cycler-independent techniques, clustered regularly interspaced short palindromic repeats-Cas-based methods, RNA-based genetic circuitry, and metagenomic next-generation sequencing for targeted or whole-genome sequencing. We also elaborate on other biosignature-based microbe detection, including phage-based detection and bioluminescent sensors for pathogen detection. The comparative advantages and disadvantages of those detection methods are reported. Finally, future perspectives for the use of these technologies in clinical and industrial settings are discussed.
The wastewater treatment sector embraces mixed-culture biotechnologies for sanitation, environmental protection, and resource recovery. Bioprocess design, monitoring and control thrive on microbial processes selected in complex microbial communities. Microbial ecology...
Aerobic granular sludge is considered one of the most promising biological wastewater treatment technologies of the 21st century. However, the long granulation time and poor treatment effect on N and P have severely limited its popularity and large-scale application. In this study, we systematically examine the strengthening effects of zeolite powder on granulation, N and P removal, and their interaction mechanisms. The addition of zeolite powder decreased sludge granulation time to 18 d, and improved average N and P removal rates by 4.48% and 2.22%, respectively. The multi-pore and nutrient-rich environment of the zeolite powder is beneficial for maintaining microbial activity and granular stability. Moreover, its adsorption to N and P enriches their respective removal strains, improving their removal efficiency.
Mittlerweile stützen sich Identifizierung und Klassifizierung weitgehend auf Sequenzanalysen von ribosomaler RNA (rRNA) beziehungsweise der diese kodierenden rDNA sowie von Genen universell verbreiteter Enzyme, da dies zu phylogenetisch korrekteren taxonomischen Gruppierungen führt als traditionelle Methoden und da auch sehr entfernte Verwandtschaften analysierbar sind. Im Folgenden sollen deshalb die Prinzipien hinter den wichtigsten molekulargenetischen Methoden zur Identifizierung und Klassifizierung von isolierten Bakterien und zur Charakterisierung mikrobieller Lebensgemeinschaften kurz dargestellt werden.
The remarkable increase in population day by day has turned the world into food hunting ground due to global food crises. Millions of people suffer from hunger and malnutrition. This claims the lives of people every year since fixed amount of land is available for farming. The realistic solution to this problem lies to utilize this available arable land to its fullest so as to meet ever increasing demand of food due to population growth. Although agricultural yield of crops should also increase as by 2050 food demands will get doubled. Change in climate is quite evident which is perceived by crops. It can further worsen this problem as temperature fluctuations cause the decline in yield of crops. So, stabilizing the population turns out to be the very daunting task. Plant with desired characters should be raised that should have the capability to withstand biotic and abiotic stresses which can be attained by using conventional breeding techniques but it is very time-consuming process. One way to circumvent all the hurdles is to make use of genetically modified crops. This technology assists the crops to grow much more at local level thereby helping to deal with global food crisis. These genetically modified crops tend to grow at fast rate than indigenous varieties. Moreover, it mitigates the food crisis along with poverty via increase in income of poor farmers. As per reports, genetically modified organisms (GMO) reduce the emission of greenhouse gases and pesticide usage. Both greenhouse gases and pesticides have very negative effect on environment. So, by reducing these harmful entities it paves the way for overall sustainable development. These genetically modified crops turn out to be not less than a magical wand having capability to tackle problems that world faces due to climate change and food crisis.
In recent years, the current problems related to fossil fuel use have led to focus on efforts to generate renewable energy sources in a clean and efficient manner.
Microalgae are an alternative for biogas generation through anaerobic digestion due to their biological, biochemical and cultural characteristics.
The efficiency and stability of anaerobic digestion is completely dependent on the microorganisms’ coordination and efficient activity as they belong to the different functional guilds, which carry hydrolysis, fermentation, acetogenesis and methanogenesis phases. In the last decade, molecular tools allow us to study anaerobic digestion phases to model and optimize the digesters’ operation when use microalgae biomass as a substrate. Studying microbial diversity and structure is important not only for basic scientific research, but also to understand the link that exists between the diversity, structure and function of the community to produce biogas.
It is not only relevant to know who is involved in the anaerobic digestion, but also what type of function it meets and at what levels of the process. This is especially relevant for the development of strategies to improve biogas production.
Logistics and scientific activities carried out in Antarctic stations entail the risk of contamination by fuels. Among remediation strategies, biostimulation of chronically contaminated Antarctic soils significantly improves the efficiency of hydrocarbons (HCs) removal. The aim of this study was to evaluate the performance of different nutrient formulations as biostimulation agents, in order to improve the elimination of diesel fuel from Antarctic soils, in both oxic and anoxic conditions. A field test was performed in microcosms (15 kg of soil each) as experimental systems. Each microcosm was prepared by triplicate, sampled every 10 days over a 50-days period and sampled again one year later. Changes in bacterial communities, and qualitative and quantitative HCs analysis were determined. Our results showed that, during the early stages of the process, a multi-component commercial product like OSEII® containing nutrients, enzymes and surfactants) determines a rapid elimination of HCs with changes in the structure of the bacterial soil community, whereas a more cost-effective slow-release fertilizer like Nitrofoska® would be efficient in a long-term bioremediation process.
454-Pyrosequencing and lipid fingerprinting were used to link anaerobic digestion (AD) process parameters (pH, alkalinity, volatile fatty acids (VFAs), biogas production and methane content) with the reactor microbial community structure and composition. AD microbial communities underwent stress conditions after changes in organic loading rate and digestion substrates. 454-Pyrosequencing analysis showed that, irrespectively of the substrate digested, methane content and pH were always significantly, and positively, correlated with community evenness. In AD, microbial communities with more even distributions of diversity are able to use parallel metabolic pathways and have greater functional stability; hence, they are capable of adapting and responding to disturbances. In all reactors, a decrease in methane content to b30% was always correlated with a 50% increase of Firmicutes sequences (particularly in operational taxonomic units (OTUs) related to Ruminococcaceae and Veillonellaceae). Whereas digesters producing higher methane content (above 60%), contained a high number of sequences related to Synergistetes and unidentified bacterial OTUs. Finally, lipid fingerprinting demonstrated that, under stress, the decrease in archaeal biomass was higher than the bacterial one, and that archaeal Phospho-lipid etherlipids (PLEL) levels were correlated to reactor performances. These results demonstrate that, across a number of parameters such as lipids, alpha and beta diversity, and OTUs, knowledge of the microbial community structure can be used to predict, monitor, or optimise AD performance. Editor: D. Barcelo
Synthetic microbial communities are attractive for applied biotechnology and healthcare applications through their ability to efficiently partition complex metabolic functions. By pairing auxotrophic mutants in co-culture, nascent E. coli communities can be established where strain pairs are metabolically coupled. Intuitive synthetic communities have been demonstrated, but the full space of cross-feeding metabolites has yet to be explored. A novel algorithm, OptAux, was constructed to design 66 multi-knockout E. coli auxotrophic strains that require significant metabolite cross-feeding when paired in co-culture. Three OptAux predicted auxotrophic strains were co-cultured with an L-histidine auxotroph and validated via adaptive laboratory evolution (ALE). Time-course sequencing revealed the genetic changes employed by each strain to achieve higher community fitness and provided insights on mechanisms for sharing and adapting to the syntrophic niche. A community model of metabolism and gene expression was utilized to predict the relative community composition and fundamental characteristics of the evolved communities. This work presents a novel computational method to elucidate metabolic changes that empower community formation and thus guide the optimization of co-cultures for a desired application.
Human activities and industrial processes have led to worldwide heavy metal pollution. Several strategies have been developped for metal remediation. The conventional strategies are expensive, usually low in efficiency and may alter the soil nature. Here we review bioremediation using plants, microbes, e.g. bacteria, fungi, and actinobacteria, earthworms, and algae for metal removal. Bioaugmentation of microbes using plants, earthworms and algae is used to enhance the bioremediation efficiency. We discuss the importance of metagenomics, metabolomics and proteomics approach to assess the response of the living organisms under stress and how they can contribute to the improvement of the already existing strategies.
Research with a laboratory prototype and at the pilot scale documents that the hydrogen-based hollow-fiber membrane-biofilm reactor (HFMBfR) is technically and economically feasible for reduction of nitrate and perchlorate. In the HFMBfR, H2 gas diffuses through the wall of a composite membrane, and an autotrophic biofilm naturally develops on the outside of the membrane, where the bacteria's electron acceptor is an oxidized contaminant (e.g., NO3 - or ClO4 - ) supplied from the water. The hydrogen pressure to the hollow fibers is a key control parameter that can be adjusted rapidly and easily. For denitrification, partial nitrate removal often is acceptable, and the hydrogen pressure can be low to minimize the costs of H2 supply and the concentration of H2 in the effluent. When perchlorate must be reduced, full nitrate removal is essential, since NO3 - -N above about 0.2 mg/L slows perchlorate reduction. Perchlorate reduction is sensitive to the hydrogen pressure, which underscores the critical role of H2 pressure for controlling process performance. Given that H2-oxidizing microorganisms have the potential to reduce many oxidized contaminants, we hypothesize that and are beginning to test how well the HFMBfR reduces bromate, selenate, chlorinated solvents, and other oxidized contaminants.
Attempts to unveil the relationships between the taxonomic diversity, productivity and stability of ecosystems continue to generate inconclusive, contradictory and controversial conclusions. New insights from recent studies support the hypothesis that species diversity enhances productivity and stability in some ecosystems, but not in others. Appreciation is growing for the ways that particular ecosystem features, such as environmental variability and nutrient stress, can influence biotic interactions. Alternatives to the diversity-stability hypothesis have been proposed, and experimental approaches are starting to evolve to test these hypotheses and to elucidate the mechanisms underlying the functional role of species diversity.
The frequent discrepancy between direct microscopic counts and numbers of culturable bacteria from environmental samples is just one of several indications that we currently know only a minor part of the diversity of microorganisms in nature. A combination of direct retrieval of rRNA sequences and whole-cell oligonucleotide probing can be used to detect specific rRNA sequences of uncultured bacteria in natural samples and to microscopically identify individual cells. Studies have been performed with microbial assemblages of various complexities ranging from simple two-component bacterial endosymbiotic associations to multispecies enrichments containing magnetotactic bacteria to highly complex marine and soil communities. Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts. For the analysis of complex communities such as multispecies biofilms and activated-sludge flocs, a different approach has proven advantageous. Sets of probes specific to different taxonomic levels are applied consecutively beginning with the more general and ending with the more specific (a hierarchical top-to-bottom approach), thereby generating increasingly precise information on the structure of the community. Not only do rRNA-targeted whole-cell hybridizations yield data on cell morphology, specific cell counts, and in situ distributions of defined phylogenetic groups, but also the strength of the hybridization signal reflects the cellular rRNA content of individual cells. From the signal strength conferred by a specific probe, in situ growth rates and activities of individual cells might be estimated for known species. In many ecosystems, low cellular rRNA content and/or limited cell permeability, combined with background fluorescence, hinders in situ identification of autochthonous populations. Approaches to circumvent these problems are discussed in detail.
Ribosomal DNA sequence analysis, originally conceived as a way to provide a universal phylogeny for life forms, has proven
useful in many areas of biological research. Some of the most promising applications of this approach are presently limited
by the rate at which sequences can be analyzed. As a step toward overcoming this limitation, we have investigated the use
of photolithography chip technology to perform sequence analyses on amplified small-subunit rRNA genes. The GeneChip (Affymetrix
Corporation) contained 31,179 20-mer oligonucleotides that were complementary to a subalignment of sequences in the Ribosomal
Database Project (RDP) (B. L. Maidak et al., Nucleic Acids Res. 29:173-174, 2001). The chip and standard Affymetrix software were able to correctly match small-subunit ribosomal DNA amplicons
with the corresponding sequences in the RDP database for 15 of 17 bacterial species grown in pure culture. When bacteria collected
from an air sample were tested, the method compared favorably with cloning and sequencing amplicons in determining the presence
of phylogenetic groups. However, the method could not resolve the individual sequences comprising a complex mixed sample.
Given these results and the potential for future enhancement of this technology, it may become widely useful.
A DNA microarray to monitor the expression of bacterial metabolic genes within mixed microbial communities was designed and
tested. Total RNA was extracted from pure and mixed cultures containing the 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading
bacterium Ralstonia eutropha JMP134, and the inducing agent 2,4-D. Induction of the 2,4-D catabolic genes present in this organism was readily detected
4, 7, and 24 h after the addition of 2,4-D. This strain was diluted into a constructed mixed microbial community derived from
a laboratory scale sequencing batch reactor. Induction of two of five 2,4-D catabolic genes (tfdA and tfdC) from populations of JMP134 as low as 105 cells/ml was clearly detected against a background of 108 cells/ml. Induction of two others (tfdB and tfdE) was detected from populations of 106 cells/ml in the same background; however, the last gene, tfdF, showed no significant induction due to high variability. In another experiment, the induction of resin acid degradative
genes was statistically detectable in sludge-fed pulp mill effluent exposed to dehydroabietic acid in batch experiments. We
conclude that microarrays will be useful tools for the detection of bacterial gene expression in wastewaters and other complex
systems.
Identifying microorganisms responsible for recognized environmental processes remains a great challenge in contemporary microbial
ecology. Only in the last few years have methodological innovations provided access to the relationship between the function
of a microbial community and the phylogeny of the organisms accountable for it. In this study stable-isotope-labeled [13C]phenol was fed into a phenol-degrading community from an aerobic industrial bioreactor, and the 13C-labeled RNA produced was used to identify the bacteria responsible for the process. Stable-isotope-labeled RNA was analyzed
by equilibrium density centrifugation in concert with reverse transcription-PCR and denaturing gradient gel electrophoresis.
In contradiction with findings from conventional methodologies, this unique approach revealed that phenol degradation in the
microbial community under investigation is dominated by a member of the Thauera genus. Our results suggest that this organism is important for the function of this bioreactor.
Bacteria may be one of the most abundant and species-rich groups of organisms, and they mediate many critical ecosystem processes. Despite the ecological importance of bacteria, past practical and theoretical constraints have limited our ability to document patterns of bacterial diversity and to understand the processes that determine these patterns. However, recent advances in molecular techniques that allow more thorough detection of bacteria in nature have made it possible to examine such patterns and processes. Here, we review recent studies of the distribution of free-living bacterial diversity and compare our current understanding with what is known about patterns in plant and animal diversity. From these recent studies a preliminary picture is emerging: bacterial diversity may exhibit regular patterns, and in some cases these patterns may be qualitatively similar to those observed for plants and animals.
The detection and monitoring of bacterial gene expression in the environment have become integral aspects of microbial ecology, bioremediation, and diversity monitoring. The rela- tively recent introduction of molecular techniques for quanti- fication of gene expression from complex environmental sam- ples has started to create a greater understanding of the roles and diversity of many bacterial populations. However, to date it is estimated that only 1% of environmental microbes has been identified and cultivated (3). This small percentage has been partially attributed to cumbersome culture techniques, the unculturability of many microbes, and the slow progression of molecular tools into environmental analysis, which has hin- dered research in this field. The resurgence of the application of molecular tools for expression analysis from environmental sources is generally seen as a consequence of reduced technol- ogy costs, together with more effective methods for recovery of nucleic acids from environmental samples (83) and increasing amounts of data on the quantitative systems that are available. Applications are wide ranging, from quantitative analysis of rRNA genes in microbial communities (10) to detection of specific pathogens (54, 55) and quantification of specific genes involved in biodegradative processes (59). Various methods that have been used to quantify mRNA from environmental samples include in situ hybridization tech- niques (2, 10, 23, 84), RNase protection assays (93, 101), Northern blotting (105), and reverse transcription (RT)-PCR (1, 71). Indeed, many of these techniques are still used fre- quently for gene expression analysis in both prokaryotic and eukaryotic systems. In theory each of the above-mentioned techniques can be used in conjunction with other techniques and assays to detect specific RNAs and precisely determine expression levels. Northern blotting is the only method that will provide information regarding transcript size and the in- tegrity of RNA samples, whereas RNase protection assays of- fer the easiest way to simultaneously examine multiple mes- sages. In situ hybridization can be used to localize expression of a specific gene(s) to a given cell but remains the most complex of all methods. RT-PCR permits analysis of gene expression at the level of a single cell and can be conducted on a large number of samples and many different genes in the same experiment (98). The one major disadvantage of standard RT-PCR with respect to other mRNA detection techniques such as Northern blot- ting is that it is only semiquantitative because of the kinetics of PCR product accumulation. Consequently, there is no linearity in the relationship between product yield and the initial tem- plate concentration (32, 34, 108). As RT-PCR offers the most sensitive and flexible method for detecting expression of indi- vidual or multiple genes, it has been increasingly coupled with various other strategies for absolute quantification. In compet- itive RT-PCR (cRT-PCR), known amounts of an internal stan- dard are coamplified in the same reaction tube with a sequence of interest, allowing the expression levels of the gene(s) under investigation to be determined (32).
We have applied “whole-genome shotgun sequencing” to microbial populations collected en masse on tangential flow and impact
filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant
sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms
within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence
relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown
genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present
and stoichiometry suggests substantial oceanic microbial diversity.
Dehalococcoides sp. strain BAV1 couples growth with the reductive dechlorination of vinyl chloride (VC) to ethene. Degenerate primers targeting
conserved regions in reductive dehalogenase (RDase) genes were designed and used to PCR amplify putative RDase genes from
strain BAV1. Seven unique RDase gene fragments were identified. Transcription analysis of VC-grown BAV1 cultures suggested
that bvcA was involved in VC reductive dechlorination, and the complete sequence of bvcA was obtained. bvcA was absent in Dehalococcoides isolates that failed to respire VC, yet was detected in four of eight VC-respiring mixed cultures.
Previous studies have suggested that members of the Geobacteraceae can use electrodes as electron acceptors for anaerobic respiration. In order to better understand this electron transfer process for energy production, Geobacter sulfurreducens was inoculated into chambers in which a graphite electrode served as the sole electron acceptor and acetate or hydrogen was the electron donor. The electron-accepting electrodes were maintained at oxidizing potentials by connecting them to similar electrodes in oxygenated medium (fuel cells) or to potentiostats that poised electrodes at +0.2 V versus an Ag/AgCl reference electrode (poised potential). When a small inoculum of G. sulfurreducens was introduced into electrode-containing chambers, electrical current production was dependent upon oxidation of acetate to carbon dioxide and increased exponentially, indicating for the first time that electrode reduction supported the growth of this organism. When the medium was replaced with an anaerobic buffer lacking nutrients required for growth, acetate-dependent electrical current production was unaffected and cells attached to these electrodes continued to generate electrical current for weeks. This represents the first report of microbial electricity production solely by cells attached to an electrode. Electrode-attached cells completely oxidized acetate to levels below detection (<10 micro M), and hydrogen was metabolized to a threshold of 3 Pa. The rates of electron transfer to electrodes (0.21 to 1.2 micro mol of electrons/mg of protein/min) were similar to those observed for respiration with Fe(III) citrate as the electron acceptor (E(o)' =+0.37 V). The production of current in microbial fuel cell (65 mA/m(2) of electrode surface) or poised-potential (163 to 1,143 mA/m(2)) mode was greater than what has been reported for other microbial systems, even those that employed higher cell densities and electron-shuttling compounds. Since acetate was completely oxidized, the efficiency of conversion of organic electron donor to electricity was significantly higher than in previously described microbial fuel cells. These results suggest that the effectiveness of microbial fuel cells can be increased with organisms such as G. sulfurreducens that can attach to electrodes and remain viable for long periods of time while completely oxidizing organic substrates with quantitative transfer of electrons to an electrode.
This study investigated a microfluidic chip-based system (on-chip flow cytometry) for quantification of bacteria both in culture
and in environmental samples. Bacterial numbers determined by this technique were similar to those obtained by direct microscopic
count. The time required for this on-chip flow cytometry was only 30 min per 6 samples.
Using genomic and mass spectrometry-based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests that damage to biomolecules is a key challenge for survival. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.
Rhinoviruses are major causes of morbidity in patients with respiratory diseases; however, their modes of transmission are controversial. We investigated detection of airborne rhinovirus in office environments by polymerase chain reaction technology and related detection to outdoor air supply rates. We sampled air from 9 A.M. to 5 P.M. each workday, with each sample run for 1 work week. We directly extracted RNA from the filters for nested reverse transcriptase-polymerase chain reaction analysis of rhinovirus. Nasal lavage samples from building occupants with upper respiratory infections were also collected. Indoor carbon dioxide (CO2 concentrations were recorded every 10 minutes as a surrogate for outdoor air supply. To increase the range of CO2 concentrations, we adjusted the outdoor air supply rates every 3 months. Generalized additive models demonstrated an association between the probability of detecting airborne rhinovirus and a weekly average CO2 concentration greater than approximately 100 ppm, after controlling for covariates. In addition, one rhinovirus from a nasal lavage contained an identical nucleic acid sequence similar to that in the building air collected during the same week. These results suggest that occupants in buildings with low outdoor air supply may have an increased risk of exposure to infectious droplet nuclei emanating from a fellow building occupant.
The frequent discrepancy between direct microscopic counts and numbers of culturable bacteria from environmental samples is just one of several indications that we currently know only a minor part of the diversity of microorganisms in nature. A combination of direct retrieval of rRNA sequences and whole-cell oligonucleotide probing can be used to detect specific rRNA sequences of uncultured bacteria in natural samples and to microscopically identify individual cells. Studies have been performed with microbial assemblages of various complexities ranging from simple two-component bacterial endosymbiotic associations to multispecies enrichments containing magnetotactic bacteria to highly complex marine and soil communities. Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts. For the analysis of complex communities such as multispecies biofilms and activated-sludge flocs, a different approach has proven advantageous. Sets of probes specific to different taxonomic levels are applied consecutively beginning with the more general and ending with the more specific (a hierarchical top-to-bottom approach), thereby generating increasingly precise information on the structure of the community. Not only do rRNA-targeted whole-cell hybridizations yield data on cell morphology, specific cell counts, and in situ distributions of defined phylogenetic groups, but also the strength of the hybridization signal reflects the cellular rRNA content of individual cells. From the signal strength conferred by a specific probe, in situ growth rates and activities of individual cells might be estimated for known species. In many ecosystems, low cellular rRNA content and/or limited cell permeability, combined with background fluorescence, hinders in situ identification of autochthonous populations. Approaches to circumvent these problems are discussed in detail.
Using genomic and mass spectrometry–based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests that damage to biomolecules is a key challenge for survival. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.
In the past 20 years, inorganic fuel cells have been transformed from novelty devices to practical energy transfer-energy storage units. However, the advantage of the high operating efficiency afforded by these fuel cells is partially offset by (a) the limited viability and high cost of the catalysts, (b) the highly corrosive electrolytes, and (c) the elevated operating temperatures. The possibility exists to reduce some of these problems through the development of bioelectrochemical fuel cells. Such biological/electrochemical systems incorporate either microorganisms or enzymes as an active component within the specified electrode compartments. Recent studies with microorganisms as part of the anode compartment have been aimed at defining the mechanism of the observed electrochemical reactions. Recent investigations on the use of cell-free enzyme preparations in the electrode compartments have dealt primarily with developing methodology and defining mechanisms for enhancing the rate of electron transfer from the enzyme-cofactor active site to the solid electrode surface. Applications of this developing technology have been envisioned for analytical chemistry, medical devices, energy transfer, electrochemical synthesis, and detoxification. In this review, the theory and problems of bioelectrochemical fuel cells are described and related to research, both recent and proposed, for the practical development of this area.
Recombinant DNA methodology and rapid nucleotide sequence determinations have changed the face of cell biology in the past few years. This technology offers powerful new tools to the microbial ecologist as well. In this chapter we describe technical strategies we are developing which use these methods to analyze phylogenetic and quantitative aspects of mixed, naturally occurring microbial populations.
Mycobacterium tuberculosis infection remains one of the major public health issues worldwide. Current qualitative assays (only positive or negative results) do not provide comprehensive information regarding health risk of M. tuberculosis. This study attempted to develop a quantitative assay to measure air concentration of M. tuberculosis in a health care setting.A total of 22 air samples were taken from the negative pressure isolation rooms of tuberculosis patients. The air was filtered through a Nuclepore filter with sampling time of 8 h. The DNA of M. tuberculosisin these airborne samples was then analyzed by the ABI 7700 real-time quantitative polymerase chain reaction (real-time qPCR) system.The real-time qPCR method could perform measurements of counts in a dynamic range of over 6 orders with a high sensitivity. The measured M. tuberculosis concentrations varied widely, from 1.43 × 10 copies/m to 2.06 × 10 copies/m. Comparisons among airborne M. tuberculosis levels, sputum smear, results, and sputum culture results showed moderate correlations.The filter/real-time qPCR method proved extremely sensitive and rapid for quantifying airborne M. tuberculosis. In addition, it is a powerful sampling tool that has potential applications as an investigational device, which might be valuable in conducting studies that validate the efficacy of engineering controls and work practices.
Direct electron transfer from different Shewanella putrefaciens strains to an electrode was examined using cyclic voltammetry and a fuel cell type electrochemical cell. Both methods determine the electrochemical activity of the bacterium without any electrochemical mediators. In the cyclic voltammetric studies, anaerobically grown cells of Shewanella putrefaciens MR-1, IR-1, and SR-21 showed electrochemical activities, but no activities were observed in aerobically grown Shewanella putrefaciens cells nor in aerobically and anaerobically grown E. coli cell suspensions. The electrochemical activities measured by the cyclic voltammetric method were closely related to the electric potential and current generation capacities in the microbial fuel cell system. Cytochromes localized to the outer membrane are believed to facilitate the direct electron transfer to the electrode from the intact bacterial cells. The concentration of the electron donor in the anode compartment determined the current generation capacity and potential development in the microbial fuel cell. When the high concentration of the bacteria (0.47 g dry cell weight/liter) and an electrode that has large surface area (apparent area: 50 cm2) were used, relatively high Coulombic yield (over 3 C for 12 h) was obtained from the bacteria.
The application of modern molecular techniques has led to the identification, in situ quantification, and partial ecophysiological characterisation of bacteria responsible for bulking and foaming or for nutrient removal in sewage treatment systems. Unexpectedly, previously unrecognised, yet uncultured bacteria were demonstrated to catalyse nitrogen and phosphorous removal in activated-sludge and biofilm reactors. These findings provide the basis for the development of novel concepts for improving the efficiency and functional stability of waste water treatment systems.
Methods derived from molecular biology provide powerful new tools to analyze biological treatment processes. Because molecular methods can be used to directly interrogate genetic information about the microbial community, they can provide the fine detail that is impossible with the blunt, nondiscriminating information usually obtained from more traditional measures such as biochemical oxygen demand and volatile suspended solids. Molecular methods allow tracking of critical groups of microorganisms, such as ammonia oxidizers, that comprise a small fraction of the total biomass. Molecular methods also allow tracking of specific metabolic reactions or other functions that are key to the satisfactory performance of a system. Despite their power, molecular methods do not provide sufficient information when used alone. Aggregated measures and quantitative modeling remain necessary to establish mass balances, quantify the function of the microbial community, and connect the results of molecular assays to practice. Several examples involving nitrifying bacteria in activated sludge illustrate the fine detail available with molecular methods and how they can be linked to traditional and quantitative analyses. Other manuscripts in this special issue also provide examples of the value of using molecular tools in combination with traditional methods.
A laboratory microcosm study and a pilot scale field test were conducted to evaluate biostimulation and bioaugmentation to dechlorinate tetrachloroethene (PCE) to ethene at Kelly Air Force Base. The site groundwater contained about 1 mg/L of PCE and lower amounts of trichloroethene (TCE) and cis-1,2-dichloroethene (cDCE). Laboratory microcosms inoculated with soil and groundwater from the site exhibited partial dechlorination of TCE to cDCE when amended with lactate or methanol. Following the addition of a dechlorinating enrichment culture, KB-1, the chlorinated ethenes in the microcosms were completely converted to ethene. The KB-1 culture is a natural dechlorinating microbial consortium that contains phylogenetic relatives of Dehalococcoides ethenogenes. The ability of KB-1 to stimulate biodegradation of chlorinated ethenes in situ was explored using a closed loop recirculation cell with a pore volume of approximately 64 000 L. The pilot test area (PTA) groundwater was first amended with methanol and acetate to establish reducing conditions. Under these conditions, dechlorination of PCE to cDCE was observed. Thirteen liters of the KB-1 culture were then injected into the subsurface. Within 200 days, the concentrations of PCE, TICE, and cis-1,2-DCE within the PTA were all below 5 mug/L, and ethene production accounted for the observed mass loss, The maximum rates of dechlorination estimated from field data were rapid (half-lives of a few hours). Throughout the pilot test period, groundwater samples were assayed for the presence of Dehalococcoides using both a Dehalococcoides-specific PCR assay and 16S rDNA sequence information. The sequences detected in the PTA after bioaugmentation were specific to the Dehalococcoides species in the KB-1 culture. These sequences were observed to progressively increase in abundance and spread downgradient within the PTA. populated the PTA aquifer and contributed to the stimulation of dechlorination beyond cDCE to ethene.
Fluorescence in situ hybridisation with rRNA-targeted nucleic acid probes can be used to directly identify microorganisms within complex samples in a few hours and therefore has widespread application in environmental and medical microbiology. The past year has seen significant methodological improvements in fluorescence in situ hybridisation, as well as in the combination of this method with other techniques for inferring functional traits of microorganisms within their environment.
Tetrachloroethene (PCE) and trichloroethene (TCE) are ideal solvents for numerous applications, and their widespread use makes them prominent groundwater pollutants. Even more troubling, natural biotic and abiotic processes acting on these solvents lead to the accumulation of toxic intermediates (such as dichloroethenes) and carcinogenic intermediates (such as vinyl chloride). Vinyl chloride was found in at least 496 of the 1,430 National Priorities List sites identified by the US Environmental Protection Agency, and its precursors PCE and TCE are present in at least 771 and 852 of these sites, respectively. Here we describe an unusual, strictly anaerobic bacterium that destroys dichloroethenes and vinyl chloride as part of its energy metabolism, generating environmentally benign products (biomass, ethene and inorganic chloride). This organism might be useful for cleaning contaminated subsurface environments and restoring drinking-water reservoirs.
Microbial fuel cells (MFCs) have been used to produce electricity from different compounds, including acetate, lactate, and glucose. We demonstrate here that it is also possible to produce electricity in a MFC from domestic wastewater, while atthe same time accomplishing biological wastewater treatment (removal of chemical oxygen demand; COD). Tests were conducted using a single chamber microbial fuel cell (SCMFC) containing eight graphite electrodes (anodes) and a single air cathode. The system was operated under continuous flow conditions with primary clarifier effluent obtained from a local wastewater treatment plant. The prototype SCMFC reactor generated electrical power (maximum of 26 mW m(-2)) while removing up to 80% of the COD of the wastewater. Power output was proportional to the hydraulic retention time over a range of 3-33 h and to the influent wastewater strength over a range of 50-220 mg/L of COD. Current generation was controlled primarily by the efficiency of the cathode. Optimal cathode performance was obtained by allowing passive air flow rather than forced air flow (4.5-5.5 L/min). The Coulombic efficiency of the system, based on COD removal and current generation, was < 12% indicating a substantial fraction of the organic matter was lost without current generation. Bioreactors based on power generation in MFCs may represent a completely new approach to wastewater treatment. If power generation in these systems can be increased, MFC technology may provide a new method to offset wastewater treatment plant operating costs, making advanced wastewater treatment more affordable for both developing and industrialized nations.
Metabolomics is an emerging field in analytical biochemistry and can be regarded as the end point of the "omics" cascade. Whereas genomics deals with the analysis of the complete genome in order to understand the function of single genes, the majority of functional genomics studies are currently based on the analysis of gene expres- sion (transcriptomics) and comprehensive protein analysis (pro- teomics). As we are amassing knowledge of the genome, the transcriptome, and the proteome, we have largely forgotten the metabolome. However, changes in the metabolome are the ultimate answer of an organism to genetic alterations, disease, or environmen- tal influences. The metabolome is therefore most predictive of phenotype (Fiehn 2002; Weckwerth 2003). Consequently, the com- prehensive and quantitative study of metabolites, or metabolomics, is a desirable tool for either diagnosing disease or studying the effects of toxicants on phenotype. One of course wonders why metabolomics has lagged behind other "omics" technologies. Possibly this is because the number of metabolites varies dramatically based on how they are counted. Investigators also debate about what compounds are considered metabolites; for example, should vitamins or smaller peptides be included? According to a simple and widely used definition, a metabolite is any substance involved in metabolism either as a product of metabolism or necessary for metabolism. In any case 3,000 major metabolites seem a reasonable number. If we attempt a global and quantitative evaluation, the technology involved is daunting because the physical properties of the compounds are so divergent and they vary dramatically in concentration. Moreover, the metabolome is a dynamic system subjected to significant environmental influences, for example, temporal or dietary.
Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na(+)(Li(+))/H(+) antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies.
A strictly anaerobic bacterium was isolated from tetrachloroethene (PCE)-to-ethene dechlorinating microcosms established with river sediment without prior exposure to chlorinated solvents. The isolation procedure included the addition of 2-bromoethanesulfonate to select against methanogenic archaea, >50 consecutive 1-2% (v/v) transfers to reduced mineral salts medium amended with trichloroethene (TCE), acetate, and hydrogen, the addition of ampicillin, and the dilution-to-extinction principle. Culture-dependent and 16S rRNA gene-targeted approaches suggested culture purity. Microscopic examination revealed a homogeneous culture of an organism with a distinct, disc-shaped morphology. The isolate shared >99% 16S rRNA gene sequence similarity with members of the Pinellas group of the Dehalococcoides cluster, and was designated Dehalococcoides sp. strain FL2. Strain FL2 could be propagated with TCE, cis-1,2-dichloroethene (cis-DCE), or trans-DCE as the electron acceptors, acetate as the carbon source, and hydrogen as the electron donor in defined, completely synthetic medium. No other growth-supporting redox couples were identified. Trichloroethene, cis-DCE and trans-DCE were dechlorinated at rates of 27.5, 30.4 and 18.8 micromol l-1 day-1 respectively. Quantitative real-time polymerase chain reaction (PCR) with a fluorescently labelled linear hybridization probe confirmed growth with these electron acceptors, and suggested that strain FL2 captures energy from both the TCE-to-cis-DCE and 1,2-DCE-to-VC dechlorination steps. Tetrachloroethene and vinyl chloride (VC) were slowly and cometabolically dechlorinated in the presence of a growth-supporting chloroethene, but ethene formation was incomplete, even after prolonged incubation. At room temperature, strain FL2 grew with a doubling time of 2.4 days, and yielded 166.1+/-10.2 mg of protein per mole of chloride released. In the presence of excess electron acceptor, strain FL2 consumed hydrogen to a concentration of 0.061+/-0.016 nM. Dechlorination ceased following the addition of 0.5 mM sulfite, whereas sulfate (10 mM) and nitrate (5 mM) had no inhibitory effects.
Thanks to their falling prices, small footprint, technical performance, and potential for automation, membrane bioreactors (MBRs) are an attractive technology for wastewater treatment. Glen T. Daigger with CH2M HILL, Bruce E. Rittmann from Arizona State University, Samer Adham at Montgomery Watson Harza, and Gianni Andreottola of the University of Trento (Italy) outline the process a group of experts followed to reach their conclusions on whether MBRs are ready for sustainable, decentralized sanitation in both developed and developing countries.
A dissimilatory Fe(III)- and Mn(IV)-reducing microorganism was isolated from freshwater sediments of the Potomac River, Maryland. The isolate, designated GS-15, grew in defined anaerobic medium with acetate as the sole electron donor and Fe(III), Mn(IV), or nitrate as the sole electron acceptor. GS-15 oxidized acetate to carbon dioxide with the concomitant reduction of amorphic Fe(III) oxide to magnetite (Fe(3)O(4)). When Fe(III) citrate replaced amorphic Fe(III) oxide as the electron acceptor, GS-15 grew faster and reduced all of the added Fe(III) to Fe(II). GS-15 reduced a natural amorphic Fe(III) oxide but did not significantly reduce highly crystalline Fe(III) forms. Fe(III) was reduced optimally at pH 6.7 to 7 and at 30 to 35 degrees C. Ethanol, butyrate, and propionate could also serve as electron donors for Fe(III) reduction. A variety of other organic compounds and hydrogen could not. MnO(2) was completely reduced to Mn(II), which precipitated as rhodochrosite (MnCO(3)). Nitrate was reduced to ammonia. Oxygen could not serve as an electron acceptor, and it inhibited growth with the other electron acceptors. This is the first demonstration that microorganisms can completely oxidize organic compounds with Fe(III) or Mn(IV) as the sole electron acceptor and that oxidation of organic matter coupled to dissimilatory Fe(III) or Mn(IV) reduction can yield energy for microbial growth. GS-15 provides a model for how enzymatically catalyzed reactions can be quantitatively significant mechanisms for the reduction of iron and manganese in anaerobic environments.
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