Integrating ecology into biotechnology

Exploration of Toxins from a Marine Annelid: An Analysis of Phyllotoxins and Accompanying Bioactives

Proteinaceous toxins are peptides or proteins that hold great biotechnological value, evidenced by their ecological role, whether as defense or predation mechanisms. Bioprospecting using bioinformatics and omics may render screening for novel bioactives more expeditious, especially considering the immense diversity of toxin-secreting marine organisms. Eulalia sp. (Annelida: Phyllodocidae), a toxin bearing marine annelid, was recently shown to secrete cysteine-rich protein (Crisp) toxins (hitherto referred to as 'phyllotoxins') that can immobilize its prey. By analyzing and validating transcriptomic data, we narrowed the list of isolated full coding sequences of transcripts of the most abundant toxins or accompanying bioactives secreted by the species (the phyllotoxin Crisp, hyaluronidase, serine protease, and peptidases M12A, M13, and M12B). Through homology matching with human proteins, the biotechnological potential of the marine annelid's toxins and related proteins was tentatively associated with coagulative and anti-inflammatory responses for the peptidases PepM12A, SePr, PepM12B, and PepM13, and with the neurotoxic activity of Crisp, and finally, hyaluronidase was inferred to bear properties of an permeabilizing agent. The in silico analysis succeeded by validation by PCR and Sanger sequencing enabled us to retrieve cDNAs can may be used for the heterologous expression of these toxins.

The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge

The use of next-generation diagnostic tools to optimise the anaerobic digestion of municipal sewage sludge has the potential to increase renewable natural gas recovery, improve the reuse of biosolid fertilisers and help operators expand circular economies globally. This review aims to provide perspectives on the role of microbial ecology in improving digester performance in wastewater treatment plants, highlighting that a systems biology approach is fundamental for monitoring mesophilic anaerobic sewage sludge in continuously stirred reactor tanks. We further highlight the potential applications arising from investigations into sludge ecology. The principal limitation for improvements in methane recoveries or in process stability of anaerobic digestion, especially after pre-treatment or during co-digestion, are ecological knowledge gaps related to the front-end metabolism (hydrolysis and fermentation). Operational problems such as stable biological foaming are a key problem, for which ecological markers are a suitable approach. However, no biomarkers exist yet to assist in monitoring and management of clade-specific foaming potentials along with other risks, such as pollutants and pathogens. Fundamental ecological principles apply to anaerobic digestion, which presents opportunities to predict and manipulate reactor functions. The path ahead for mapping ecological markers on process endpoints and risk factors of anaerobic digestion will involve numerical ecology, an expanding field that employs metrics derived from alpha, beta, phylogenetic, taxonomic, and functional diversity, as well as from phenotypes or life strategies derived from genetic potentials. In contrast to addressing operational issues (as noted above), which are effectively addressed by whole population or individual biomarkers, broad improvement and optimisation of function will require enhancement of hydrolysis and acidogenic processes. This will require a discovery-based approach, which will involve integrative research involving the proteome and metabolome. This will utilise, but overcome current limitations of DNA-centric approaches, and likely have broad application outside the specific field of anaerobic digestion.

Organic matter- and temperature-driven deterministic assembly processes govern bacterial community composition and functionality during manure composting

Although many studies have shown that microbial communities play important roles in organic waste composting due to the involvement of specific microbial taxa with metabolic functions, the underlying ecological processes of community assembly and governing factors remain elusive. Thus, a chicken manure composting experiment as a model system of microbially mediated organic waste composting was conducted. Ecological null modeling and metabolic functional prediction combined with electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) were used to quantify assembly processes governing bacterial community composition and functions during composting. The results showed the predominant role of deterministic assembly processes in shifting community compositions both across and within composting stages. Stochastic assembly processes also concomitantly influenced microbial community compositions. Changes in the organic matter (OM) content and its chemical properties and temperature governed bacterial community assembly processes throughout the stages by selecting specific bacterial taxa such as Cardiobacteriales, Bacteroidales, and Lachnospiraceae on day 1, Firmicutes on days 6, 25 and 37, and Sphingobacteriales, Thermoactinomycetaceae, Actinobacteria, and Novibacillus on day 45. These taxa ultimately influenced community functions such as environmental information processing, carbohydrate and amino acid metabolism, cellular processes, and genetic information processes involved in composting. Taken together, this study indicates that deterministic assembly processes governed by OM content and quality as well as temperature influenced microbial community turnover and determined community functions during composting. These results are important for better understanding and predicting microbial-driven composting and for ultimately manipulating microorganisms for environmentally-friendly composting outcomes.

Balanced stochastic versus deterministic assembly processes benefit diverse yet uneven ecosystem functions in representative agroecosystems

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.

Deterministic Assembly and Diversity Gradient Altered the Biofilm Community Performances of Bioreactors

Community assembly process (determinism vs stochasticity) determines the composition and diversity of a 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 in 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 the 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.

Microbial biotechnology and circular economy in wastewater treatment

Microbial biotechnology is essential for the development of circular economy in wastewater treatment by integrating energy production and resource recovery into the production of clean water. A comprehensive knowledge about identity, physiology, ecology, and population dynamics of process‐critical microorganisms will improve process stability, reduce CO2 footprints, optimize recovery and bioenergy production, and help finding new approaches and solutions. Examples of research needs and perspectives are provided, demonstrating the great importance of microbial biotechnology.

A geographically-diverse collection of 418 human gut microbiome pathway genome databases

Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GutCyc, a compendium of environmental pathway genome databases (ePGDBs) constructed from 418 assembled human microbiome datasets using MetaPathways, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the Pathway Tools software, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GutCyc provides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn's disease, and type 2 diabetes. GutCyc data products are searchable online, or may be downloaded and explored locally using MetaPathways and Pathway Tools.

Microbial diversity of a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing

The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset. The virome characterization revealed the presence of two viral families with Bacteria and Archaea as host, Myoviridae, and Siphoviridae. A wide functional diversity was found with predominance of genes involved in the metabolism of acetone, butanol, and ethanol synthesis; and one-carbon metabolism (e.g., methanogenesis). Genes related to the acetotrophic methanogenesis pathways were more abundant than methylotrophic and hydrogenotrophic, corroborating the taxonomic results that showed the prevalence of the acetotrophic genus Methanosaeta. Moreover, the dataset indicated a variety of metabolic genes involved in sulfur, nitrogen, iron, and phosphorus cycles, with many genera able to act in all cycles. BLAST analysis against Antibiotic Resistance Genes Database (ARDB) revealed that microbial community contained 43 different types of antibiotic resistance genes, some of them were associated with growth chicken promotion (e.g., bacitracin, tetracycline, and polymyxin).

Microbial legacies alter decomposition in response to simulated global change

Terrestrial ecosystem models assume that microbial communities respond instantaneously, or are immediately resilient, to environmental change. Here we tested this assumption by quantifying the resilience of a leaf litter community to changes in precipitation or nitrogen availability. By manipulating composition within a global change experiment, we decoupled the legacies of abiotic parameters versus that of the microbial community itself. After one rainy season, more variation in fungal composition could be explained by the original microbial inoculum than the litterbag environment (18% versus 5.5% of total variation). This compositional legacy persisted for 3 years, when 6% of the variability in fungal composition was still explained by the microbial origin. In contrast, bacterial composition was generally more resilient than fungal composition. Microbial functioning (measured as decomposition rate) was not immediately resilient to the global change manipulations; decomposition depended on both the contemporary environment and rainfall the year prior. Finally, using metagenomic sequencing, we showed that changes in precipitation, but not nitrogen availability, altered the potential for bacterial carbohydrate degradation, suggesting why the functional consequences of the two experiments may have differed. Predictions of how terrestrial ecosystem processes respond to environmental change may thus be improved by considering the legacies of microbial communities.

Quorum Sensing Communication Modules for Microbial Consortia

The power of a single engineered organism is limited by its capacity for genetic modification. To circumvent the constraints of any singular microbe, a new frontier in synthetic biology is emerging: synthetic ecology, or the engineering of microbial consortia. Here we develop communication systems for such consortia in an effort to allow for complex social behavior across different members of a community. We posit that such communities will outpace monocultures in their ability to perform complicated tasks if communication among and between members of the community is well regulated. Quorum sensing was identified as the most promising candidate for precise control of engineered microbial ecosystems, due to its large diversity and established utility in synthetic biology. Through promoter and protein modification, we engineered two quorum sensing systems (rpa and tra) to add to the extensively used lux and las systems. By testing the cross-talk between all systems, we thoroughly characterized many new inducible systems for versatile control of engineered communities. Furthermore, we've identified several system pairs that exhibit useful types of orthogonality. Most notably, the tra and rpa systems were shown to have neither signal crosstalk nor promoter crosstalk for each other, making them completely orthogonal in operation. Overall, by characterizing the interactions between all four systems and their components, these circuits should lend themselves to higher-level genetic circuitry for use in microbial consortia.

Molecular characterization of a eukaryotic-like phenol hydroxylase from Corynebacterium glutamicum

This study focuses on the genetic and biochemical characterization of phenol hydroxylase (Phe, NCgl2588) from Corynebacterium glutamicum that shares 31% identity in amino acids with phenol hydroxylase from yeast Trichosporon cutaneum but less similarity with that from bacteria. The phe deletion mutant significantly reduced its ability to grow with phenol as the sole carbon and energy source. Expression of the phe gene was strongly induced with phenol and also subject to the control of carbon catabolite repression (CCR). The molecular weight of purified Phe protein determined by gel filtration chromatography was 70 kDa, indicating that Phe exists as a monomer in the purification condition. However, Phe protein pre-incubated with phenol showed a molecular weight of 140 kDa, suggesting that Phe is likely active as a dimer. In addition to phenol, the Phe protein could utilize various other phenolic compounds as substrates. Site-directed mutagenesis revealed that D75, P261, R262, R269, C349 and C476 are key amino acid residues closely related to the enzyme activity of Phe.

Microbial diversity in support of anaerobic biomass valorization

Microbial diversity provides an immense reservoir of functions and supports key steps in maintaining ecosystem balance through matter decomposition processes and nutrient recycling. The use of microorganisms for biomolecule production is now common, but often involves single-strain cultures. In this review, we highlight the significance of using ecosystem-derived microbial diversity for biotechnological researches. In the context of organic matter mineralization, diversity of microorganisms is essential and enhances the degradation processes. We focus on anaerobic production of biomolecules of interest from discarded biomass, which is an important issue in the context of organic waste valorization and processing. Organic waste represents an important and renewable raw material but remains underused. It is commonly accepted that anaerobic mineralization of organic waste allows the production of diverse interesting molecules within several fields of application. We provide evidence that complex and diversified microbial communities isolated from ecosystems, i.e. microbial consortia, offer considerable advantages in degrading complex organic waste, to yield biomolecules of interest. We defend our opinion that this approach is more efficient and offers enhanced potential compared to the approaches that use single strain cultures.

Functionally redundant but dissimilar microbial communities within biogas reactors treating maize silage in co-fermentation with sugar beet silage

Numerous observations indicate a high flexibility of microbial communities in different biogas reactors during anaerobic digestion. Here, we describe the functional redundancy and structural changes of involved microbial communities in four lab-scale continuously stirred tank reactors (CSTRs, 39°C, 12 L volume) supplied with different mixtures of maize silage (MS) and sugar beet silage (SBS) over 80 days. Continuously stirred tank reactors were fed with mixtures of MS and SBS in volatile solid ratios of 1:0 (Continuous Fermenter (CF) 1), 6:1 (CF2), 3:1 (CF3), 1:3 (CF4) with equal organic loading rates (OLR 1.25 kgVS m(-3)  d(-1) ) and showed similar biogas production rates in all reactors. The compositions of bacterial and archaeal communities were analysed by 454 amplicon sequencing approach based on 16S rRNA genes. Both bacterial and archaeal communities shifted with increasing amounts of SBS. Especially pronounced were changes in the archaeal composition towards Methanosarcina with increasing proportion of SBS, while Methanosaeta declined simultaneously. Compositional shifts within the microbial communities did not influence the respective biogas production rates indicating that these communities adapted to environmental conditions induced by different feedstock mixtures. The diverse microbial communities optimized their metabolism in a way that ensured efficient biogas production.

Impact of T-RFLP data analysis choices on assessments of microbial community structure and dynamics

Background

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a common DNA-fingerprinting technique used for comparisons of complex microbial communities. Although the technique is well established there is no consensus on how to treat T-RFLP data to achieve the highest possible accuracy and reproducibility. This study focused on two critical steps in the T-RFLP data treatment: the alignment of the terminal restriction fragments (T-RFs), which enables comparisons of samples, and the normalization of T-RF profiles, which adjusts for differences in signal strength, total fluorescence, between samples.

Results

Variations in the estimation of T-RF sizes were observed and these variations were found to affect the alignment of the T-RFs. A novel method was developed which improved the alignment by adjusting for systematic shifts in the T-RF size estimations between the T-RF profiles. Differences in total fluorescence were shown to be caused by differences in sample concentration and by the gel loading. Five normalization methods were evaluated and the total fluorescence normalization procedure based on peak height data was found to increase the similarity between replicate profiles the most. A high peak detection threshold, alignment correction, normalization and the use of consensus profiles instead of single profiles increased the similarity of replicate T-RF profiles, i.e. lead to an increased reproducibility. The impact of different treatment methods on the outcome of subsequent analyses of T-RFLP data was evaluated using a dataset from a longitudinal study of the bacterial community in an activated sludge wastewater treatment plant. Whether the alignment was corrected or not and if and how the T-RF profiles were normalized had a substantial impact on ordination analyses, assessments of bacterial dynamics and analyses of correlations with environmental parameters.

Conclusions

A novel method for the evaluation and correction of the alignment of T-RF profiles was shown to reduce the uncertainty and ambiguity in alignments of T-RF profiles. Large differences in the outcome of assessments of bacterial community structure and dynamics were observed between different alignment and normalization methods. The results of this study can therefore be of value when considering what methods to use in the analysis of T-RFLP data.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0360-8) contains supplementary material, which is available to authorized users.

Disturbance and temporal partitioning of the activated sludge metacommunity

The resilience of microbial communities to press disturbances and whether ecosystem function is governed by microbial composition or by the environment have not been empirically tested. To address these issues, a whole-ecosystem manipulation was performed in a full-scale activated sludge wastewater treatment plant. The parameter solids retention time (SRT) was used to manipulate microbial composition, which started at 30 days, then decreased to 12 and 3 days, before operation was restored to starting conditions (30-day SRT). Activated sludge samples were collected throughout the 313-day time series in parallel with bioreactor performance ('ecosystem function'). Bacterial small subunit (SSU) rRNA genes were surveyed from sludge samples resulting in a sequence library of >417,000 SSU rRNA genes. A shift in community composition was observed for 12- and 3-day SRTs. The composition was altered such that r-strategists were enriched in the system during the 3-day SRT, whereas K-strategists were only present at SRTs⩾12 days. This shift corresponded to loss of ecosystem functions (nitrification, denitrification and biological phosphorus removal) for SRTs⩽12 days. Upon return to a 30-day SRT, complete recovery of the bioreactor performance was observed after 54 days despite an incomplete recovery of bacterial diversity. In addition, a different, yet phylogenetically related, community with fewer of its original rare members displaced the pre-disturbance community. Our results support the hypothesis that microbial ecosystems harbor functionally redundant phylotypes with regard to general ecosystem functions (carbon oxidation, nitrification, denitrification and phosphorus accumulation). However, the impacts of decreased rare phylotype membership on ecosystem stability and micropollutant removal remain unknown.

Design, construction, and characterization methodologies for synthetic microbial consortia

Engineered microbial consortia are of growing interest to a range of scientists including bioprocess engineers, systems biologists, and microbiologists because of their ability to simultaneously optimize multiple tasks, to test fundamental systems science, and to understand the microbial ecology of environments like chronic wounds. Metabolic engineering, synthetic biology, and microbial ecology provide a sound scientific basis for designing, building, and analyzing consortium-based microbial platforms.This chapter outlines strategies and protocols useful for (1) in silico network design, (2) experimental strain construction, (3) consortia culturing including biofilm growth methods, and (4) physiological characterization of consortia. The laboratory and computational methods given here may be adapted for synthesis and characterization of other engineered consortia designs.

Gastrointestinal tract microbiota and probiotics in production animals

The gastrointestinal tract (GIT) microbiomes of production animals are now firmly established as a key feature underscoring animal health, development, and productivity. In particular, early gut colonization is critically important to the morphological and immunological development of the GIT, development of a functional fermentative environment, and neonatal resistance to pathogenic challenge. Although perturbations of an animal's GIT microbiome at any age can have profound consequences, perturbations during early GIT development can be particularly severe and result in significant and long-lasting sequelae. As the GIT microbiome matures, it exhibits significant diversity, ostensibly an important indicator of ecosystem health. Recognition of the immense importance of the GIT microbiota to the host has led to the development of probiotic and prebiotic feedstuffs with the express aim of ensuring animal health. We herein review the current collective understanding of the GIT microbiota of production animals.

The choice of PCR primers has great impact on assessments of bacterial community diversity and dynamics in a wastewater treatment plant

Assessments of bacterial community diversity and dynamics are fundamental for the understanding of microbial ecology as well as biotechnological applications. We show that the choice of PCR primers has great impact on the results of analyses of diversity and dynamics using gene libraries and DNA fingerprinting. Two universal primer pairs targeting the 16S rRNA gene, 27F&1492R and 63F&M1387R, were compared and evaluated by analyzing the bacterial community in the activated sludge of a large-scale wastewater treatment plant. The two primer pairs targeted distinct parts of the bacterial community, none encompassing the other, both with similar richness. Had only one primer pair been used, very different conclusions had been drawn regarding dominant phylogenetic and putative functional groups. With 27F&1492R, Betaproteobacteria would have been determined to be the dominating taxa while 63F&M1387R would have described Alphaproteobacteria as the most common taxa. Microscopy and fluorescence in situ hybridization analysis showed that both Alphaproteobacteria and Betaproteobacteria were abundant in the activated sludge, confirming that the two primer pairs target two different fractions of the bacterial community. Furthermore, terminal restriction fragment polymorphism analyses of a series of four activated sludge samples showed that the two primer pairs would have resulted in different conclusions about community stability and the factors contributing to changes in community composition. In conclusion, different PCR primer pairs, although considered universal, target different ranges of bacteria and will thus show the diversity and dynamics of different fractions of the bacterial community in the analyzed sample. We also show that while a database search can serve as an indicator of how universal a primer pair is, an experimental assessment is necessary to evaluate the suitability for a specific environmental sample.

Microbial contributions to phosphorus cycling in eutrophic lakes and wastewater

Phosphorus is a key element controlling the productivity of freshwater ecosystems, and microbes drive most of its relevant biogeochemistry. Eutrophic lakes are generally dominated by cyanobacteria that compete fiercely with algae and heterotrophs for the element. In wastewater treatment, engineers select for specialized bacteria capable of sequestering phosphorus from the water, to protect surface waters from further loading. The intracellular storage molecule polyphosphate plays an important role in both systems, allowing key taxa to control phosphorus availability. The importance of dissolved organic phosphorus in eutrophic lakes and mineralization mechanisms is still underappreciated and understudied. The need for functional redundancy through biological diversity in wastewater treatment plants is also clear. In both systems, a holistic ecosystems biology approach is needed to understand the molecular mechanisms controlling phosphorus metabolism and the ecological interactions and factors controlling ecosystem-level process rates.

Diversity of the chlorite dismutase gene in low and high organic carbon rhizosphere soil colonized by perchlorate-reducing bacteria

Chlorite dismutase (cld) is an essential enzyme in the biodegradation of perchlorate. The objective of this study was to determine the change in sequence diversity of the cld gene, and universal bacterial 16S rRNA genes, in soil samples under varying conditions of organic carbon, bioaugmentation, and plant influence. The cld gene diversity was not different between high organic carbon (HOC) and low organic carbon (LOC) soil. Combining results from HOC and LOC soil, diversity of the cld gene was decreased in soil that had been bioaugmented or planted. However, with both bioaugmentation and planting the cld diversity was not decreased. These observations were repeated when focusing on LOC soil. However, in HOC soil the cld diversity was not affected by reactor treatment. General bacterial diversity as measured with 16S rRNA was significantly greater in HOC soil than in LOC soil, but no significant difference was observed between reference soil and planted or bioaugmented soil. Different sequences of the cld gene occur in different species of microorganisms. In LOC soil, combining bioaugmentation and planting results in a highly diverse population of perchlorate degraders. This diverse population will be more resilient and is desirable where perchlorate reduction is a critical remediation process. Supplemental materials are available for this article. Go to the publisher's online edition of International Journal of Phytoremediation to view the supplemental file.

Microbial Consortia Engineering for Cellular Factories: in vitro to in silico systems

This mini-review discusses the current state of experimental and computational microbial consortia engineering with a focus on cellular factories. A discussion of promising ecological theories central to community resource usage is presented to facilitate interpretation of consortial designs. Recent case studies exemplifying different resource usage motifs and consortial assembly templates are presented. The review also highlights in silico approaches to design and to analyze consortia with an emphasis on stoichiometric modeling methods. The discipline of microbial consortia engineering possesses a widely accepted potential to generate highly novel and effective bio-catalysts for applications from biofuels to specialty chemicals to enhanced mineral recovery.

Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity

Synthetic Escherichia coli consortia engineered for syntrophy demonstrated enhanced biomass productivity relative to monocultures. Binary consortia were designed to mimic a ubiquitous, naturally occurring ecological template of primary productivity supported by secondary consumption. The synthetic consortia replicated this evolution-proven strategy by combining a glucose positive E. coli strain, which served as the system's primary producer, with a glucose negative E. coli strain which consumed metabolic byproducts from the primary producer. The engineered consortia utilized strategic division of labor to simultaneously optimize multiple tasks enhancing overall culture performance. Consortial interactions resulted in the emergent property of enhanced system biomass productivity which was demonstrated with three distinct culturing systems: batch, chemostat and biofilm growth. Glucose-based biomass productivity increased by ∼15, 20 and 50% compared to appropriate monoculture controls for these three culturing systems, respectively. Interestingly, the consortial interactions also produced biofilms with predictable, self-assembling, laminated microstructures. This study establishes a metabolic engineering paradigm which can be easily adapted to existing E. coli based bioprocesses to improve productivity based on a robust ecological theme.

Programming microbial population dynamics by engineered cell-cell communication

A major aim of synthetic biology is to program novel cellular behavior using engineered gene circuits. Early endeavors focused on building simple circuits that fulfill simple functions, such as logic gates, bistable toggle switches, and oscillators. These gene circuits have primarily focused on single-cell behaviors since they operate intracellularly. Thus, they are often susceptible to cell-cell variations due to stochastic gene expression. Cell-cell communication offers an efficient strategy to coordinate cellular behavior at the population level. To this end, we review recent advances in engineering cell-cell communication to achieve reliable population dynamics, spanning from communication within single species to multispecies, from one-way sender-receiver communication to two-way communication in synthetic microbial ecosystems. These engineered systems serve as well-defined model systems to better understand design principles of their naturally occurring counterparts and to facilitate novel biotechnology applications.

Regime shift and microbial dynamics in a sequencing batch reactor for nitrification and anammox treatment of urine

The microbial population and physicochemical process parameters of a sequencing batch reactor for nitrogen removal from urine were monitored over a 1.5-year period. Microbial community fingerprinting (automated ribosomal intergenic spacer analysis), 16S rRNA gene sequencing, and quantitative PCR on nitrogen cycle functional groups were used to characterize the microbial population. The reactor combined nitrification (ammonium oxidation)/anammox with organoheterotrophic denitrification. The nitrogen elimination rate initially increased by 400%, followed by an extended period of performance degradation. This phase was characterized by accumulation of nitrite and nitrous oxide, reduced anammox activity, and a different but stable microbial community. Outwashing of anammox bacteria or their inhibition by oxygen or nitrite was insufficient to explain reactor behavior. Multiple lines of evidence, e.g., regime-shift analysis of chemical and physical parameters and cluster and ordination analysis of the microbial community, indicated that the system had experienced a rapid transition to a new stable state that led to the observed inferior process rates. The events in the reactor can thus be interpreted to be an ecological regime shift. Constrained ordination indicated that the pH set point controlling cycle duration, temperature, airflow rate, and the release of nitric and nitrous oxides controlled the primarily heterotrophic microbial community. We show that by combining chemical and physical measurements, microbial community analysis and ecological theory allowed extraction of useful information about the causes and dynamics of the observed process instability.

Bacteriophage ecology in environmental biotechnology processes

Heterotrophic bacteria are an integral part of any environmental biotechnology process (EBP). Therefore, factors controlling bacterial abundance, activity, and community composition are central to the understanding of such processes. Among these factors, top-down control by bacteriophage predation has so far received very limited attention. With over 10(8) particles per ml, phage appear to be the most numerous biological entities in EBP. Phage populations in EBP appear to be highly dynamic and to correlate with the population dynamics of their hosts and genomic evidence suggests bacteria evolve to avoid phage predation. Clearly, there is much to learn regarding bacteriophage in EBP before we can truly understand the microbial ecology of these globally important systems.

Maintenance of phenol hydroxylase genotypes at high diversity in bioreactors exposed to step increases in phenol loading

To better understand how the composition of bacterial communities changes in response to different environmental conditions, we examined the influence of increasing phenol load on the distribution of the protein-coding functional gene of the largest subunit of phenol hydroxylase (LmPH) and of the 16S rRNA gene in lab-scale activated sludge reactors. LmPH diversity was assessed initially from a total of 124 clone sequences retrieved from two reactors exposed to a low (0.25 g L(-1)) and a high (2.5 g L(-1)) phenol concentration. The quantitative changes in the concentration of the eight detected genotypes accompanied changes in the phenol degradation rates, indicating a community structure-function relationship. Nonmetric dimensional analysis showed that LmPH genotypes and the denaturing gradient gel electrophoresis banding patterns clustered together by phenol concentration, rather than by reactor identity. Seven isolates, representing cultivated strains of each of the observed LmPH genotypes, exhibited a rather narrow range of physiological diversity, in terms of the growth rate and the kinetic parameters of the phenol-degrading activity. We suggest that lab-scale reactors support many ecological niches, which allow the maintenance of a high diversity of ecotypes through varying concentrations of phenol, but the ability of particular strains to become dominant members of the community under the different environmental conditions cannot be predicted easily solely from their phenol-degrading properties.

Nonrandom assembly of bacterial populations in activated sludge flocs

The aim of this work was to investigate the dynamics of assembly of bacterial populations in activated sludge flocs. We approached this question by following the development of active bacterial populations during floc development in four replicated lab-scale activated sludge reactors, in which solid retention time (SRT) was set at 4 days. The null hypothesis was that the similarities in community composition could be accounted for by the probability that the same organisms occur in more than one replicated reactor. Microscopic imaging showed that the size of flocs in reactors with biomass retention increased during the first few days until a steady-state size was reached. The diversity and community structure of the sludge in all reactors were analyzed during a period of up to ten SRT, using denaturing gradient gel electrophoresis (DGGE) of reverse-transcription polymerase chain reaction-amplified 16S rRNA. High rates of change in DGGE profiles from consecutive sampling points suggested a high level of dynamics in all reactors. This conclusion was confirmed by the application of the Raup and Crick probability-based similarity index (S(RC)) for the comparison of rRNA-based fingerprinting patterns, which indicated that bacterial communities within reactors were not significantly similar after three SRT (0.05 < S(RC) < 0.95) and became significantly dissimilar after five SRT (S(RC) < 0.05). More importantly, significant similarity between replicate reactors was observed at all times analyzed (S(RC) > 0.95). The fact that the patterns between replicates were more reproducible than expected by chance under highly dynamic conditions allowed us to reject the null hypothesis that activated sludge floc communities assemble randomly from the available source pool of bacteria. We suggest that communities progressively recruit from the available pool of bacterial species, each with particular ecological requirements that determine their time of emergence into the community.

Valuable processes and products from marine intertidal microbial communities

Microbial communities are ubiquitous in marine intertidal environments. These communities, which grow preferentially as biofilms on natural and artificial surfaces, carry out key processes contributing to the functioning of coastal environments and providing valuable services to human society, including carbon cycling, primary productivity, trophic linkage, and transfer and removal of pollutants. In addition, their surface-associated life style greatly influences the integrity and performance of marine infrastructure and archaeological heritage materials. The fluctuating conditions of the intertidal zone make it an extreme environment to which intertidal biofilm organisms must adapt at varying levels. This requirement has probably favored the development and spread of specific microorganisms with particular physiological and metabolic processes. These organisms may have potential biotechnological utility, in that they may provide novel secondary metabolites, biopolymers, lipids, and enzymes and even processes for the production of energy in a sustainable manner.

High reproducibility of ammonia-oxidizing bacterial communities in parallel sequential batch reactors

AIMS

To investigate whether the ammonia-oxidizing bacterial (AOB) communities of replicate nitrifying bioreactors (i) co-evolve or diverge over time and (ii) are stable or dynamic during periods of complete nitrification.

METHODS AND RESULTS

Three sequential batch reactors (SBR) were inoculated with sludge from a municipal wastewater treatment plant, fed with ammonium-enriched tap water and operated in parallel for 134 days. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) demonstrated co-evolvement of the AOB communities over time. During start-up, temporary decreases in nitrification were noticed, and the AOB community rate of change values (Delta(t(week))) were medium to high (12-22%). During the adjacent period of complete nitrification, low AOB community dynamics were observed (Delta(t(week)) < 5%). Further pragmatic processing of the DGGE profiles revealed a high range-weighted richness and a medium functional organization of the AOB communities.

CONCLUSIONS

After a start-up period, high functional stability and low dynamics of the AOB communities were observed. Deterministic rather than stochastic driving forces led to AOB community co-evolvement in the replicate SBR.

SIGNIFICANCE AND IMPACT OF THE STUDY

Replicates in identical set-ups are reproducible, and pragmatic processing of DGGE patterns is a straightforward tool to score and compare the functionality of the bacterial communities.

Bacterial community dynamics in an anaerobic plug-flow type bioreactor treating swine manure

A plug-flow type anaerobic reactor consisting of eight sequential compartments was used to study shifts in a bacterial community adapted to degrade swine manure at 25 degrees C. The investigation was carried out during the first 6 months of reactor operation. The reactor successfully separated the hydrolysis/acidogenesis stage from the methanogenesis stage. Bacterial 16S rDNA- and rRNA-based fingerprints obtained through amplicon length heterogeneity PCR (LH-PCR) were analyzed with a view to characterizing the bacterial community structure and the metabolically active community, respectively. Multivariate statistical tools showed that the rDNA-based fingerprints described a more temporal than compartmentalized distribution of similar bacterial communities. By contrast, the rRNA-based multivariate analyses described a distribution that was linked more to reactor performance parameters, especially during short time periods. Diversity indices calculated from fingerprint data were used to assess overall diversity shifts. The decrease in rRNA-based diversity observed through the reactor compartments was greater than the decrease in rDNA-based diversity. This finding indicates that the analysis of metabolically active bacteria diversity was more discriminative than the analysis based on the mere presence of bacteria. The observed decrease in diversity suggests that the bacterial community became specialized in degrading less diversified substrates through the compartments. All these findings suggest that rRNA-based analyses are more appropriate for monitoring reactor performance.

Effect of anoxic selector configuration on sludge volume index control and bacterial population fingerprinting

The effect of single-stage and 4-stage anoxic selectors and an anoxic/aerobic sequencing batch reactor (SBR) on the removal of readily biodegradable chemical oxygen demand (rbCOD) and slowly biodegradable COD (sbCOD) and on filamentous growth and sludge settleability was studied. Microbial community fingerprinting in the three selector configurations was done using automated ribosomal intergenic spacer analysis. Nostocoida limicola II and type 1851 filamentous bacteria were observed in all systems. The diluted sludge volume index (DSVI) decreased with increased selector staging. The rbCOD was almost completely removed in all selectors, and the lower DSVI values with increased selector staging were the result of greater sbCOD removal in the selector. The plug-flow kinetics in the SBR aerobic phase also improved DSVI. The bacteria community composition in the 4-stage selector system was found to be more similar to that for the SBR than for the single-stage selector.