Showing papers in "Fems Microbiology Letters in 2018"

Vector-borne diseases and climate change: a European perspective.

Abstract: Climate change has already impacted the transmission of a wide range of vector-borne diseases in Europe, and it will continue to do so in the coming decades. Climate change has been implicated in the observed shift of ticks to elevated altitudes and latitudes, notably including the Ixodes ricinus tick species that is a vector for Lyme borreliosis and tick-borne encephalitis. Climate change is also thought to have been a factor in the expansion of other important disease vectors in Europe: Aedes albopictus (the Asian tiger mosquito), which transmits diseases such as Zika, dengue and chikungunya, and Phlebotomus sandfly species, which transmits diseases including Leishmaniasis. In addition, highly elevated temperatures in the summer of 2010 have been associated with an epidemic of West Nile Fever in Southeast Europe and subsequent outbreaks have been linked to summer temperature anomalies. Future climate-sensitive health impacts are challenging to project quantitatively, in part due to the intricate interplay between non-climatic and climatic drivers, weather-sensitive pathogens and climate-change adaptation. Moreover, globalisation and international air travel contribute to pathogen and vector dispersion internationally. Nevertheless, monitoring forecasts of meteorological conditions can help detect epidemic precursors of vector-borne disease outbreaks and serve as early warning systems for risk reduction.

Ammonia oxidation: Ecology, physiology, biochemistry and why they must all come together.

Abstract: Ammonia oxidation is a fundamental core process in the global biogeochemical nitrogen cycle. Oxidation of ammonia (NH3) to nitrite (NO2 −) is the first and rate-limiting step in nitrification and is carried out by distinct groups of microorganisms. Ammonia oxidation is essential for nutrient turnover in most terrestrial, aquatic and engineered ecosystems and plays a major role, both directly and indirectly, in greenhouse gas production and environmental damage. Although ammonia oxidation has been studied for over a century, this research field has been galvanised in the past decade by the surprising discoveries of novel ammonia oxidising microorganisms. This review reflects on the ammonia oxidation research to date and discusses the major gaps remaining in our knowledge of the biology of ammonia oxidation.

Bacterial type III secretion systems: a complex device for the delivery of bacterial effector proteins into eukaryotic host cells.

Abstract: Virulence-associated type III secretion systems (T3SS) serve the injection of bacterial effector proteins into eukaryotic host cells. They are able to secrete a great diversity of substrate proteins in order to modulate host cell function, and have evolved to sense host cell contact and to inject their substrates through a translocon pore in the host cell membrane. T3SS substrates contain an N-terminal signal sequence and often a chaperone-binding domain for cognate T3SS chaperones. These signals guide the substrates to the machine where substrates are unfolded and handed over to the secretion channel formed by the transmembrane domains of the export apparatus components and by the needle filament. Secretion itself is driven by the proton motive force across the bacterial inner membrane. The needle filament measures 20-150 nm in length and is crowned by a needle tip that mediates host-cell sensing. Secretion through T3SS is a highly regulated process with early, intermediate and late substrates. A strict secretion hierarchy is required to build an injectisome capable of reaching, sensing and penetrating the host cell membrane, before host cell-acting effector proteins are deployed. Here, we review the recent progress on elucidating the assembly, structure and function of T3SS injectisomes.

Scale-up of industrial microbial processes

Abstract: Scaling up industrial microbial processes for commercial production is a high-stakes endeavor, requiring time and investment often exceeding that for laboratory microbe and process development. Omissions, oversights and errors can be costly, even fatal to the program. Approached properly, scale-up can be executed successfully. Three guiding principles are provided as a basis: begin with the end in mind; be diligent in the details; prepare for the unexpected. A detailed roadmap builds on these principles. There is a special emphasis on the fermentation step, which is usually the costliest and also impacts downstream processing. Examples of common scale-up mistakes and the recommended approaches are given. It is advised that engineering resources skilled in integrated process development and scale-up be engaged from the very beginning of microbe and process development to guide ongoing R&D, thus ensuring a smooth and profitable path to the large-scale commercial end.

Lactic acid bacteria: from starter cultures to producers of chemicals.

Abstract: Lactic acid bacteria constitute a diverse group of industrially significant, safe microorganisms that are primarily used as starter cultures and probiotics, and are also being developed as production systems in industrial biotechnology for biocatalysis and transformation of renewable feedstocks to commodity- and high-value chemicals, and health products Development of strains, which was initially based mainly on natural approaches, is also achieved by metabolic engineering that has been facilitated by the availability of genome sequences and genetic tools for transformation of some of the bacterial strains The aim of this paper is to provide a brief overview of the potential of lactic acid bacteria as biological catalysts for production of different organic compounds for food and non-food sectors based on their diversity, metabolic- and stress tolerance features, as well as the use of genetic/metabolic engineering tools for enhancing their capabilities

State of the art in eukaryotic nitrogenase engineering.

Abstract: Improving the ability of plants and plant-associated organisms to fix and assimilate atmospheric nitrogen has inspired plant biotechnologists for decades, not only to alleviate negative effects on nature from increased use and availability of reactive nitrogen, but also because of apparent economic benefits and opportunities. The combination of recent advances in synthetic biology and increased knowledge about the biochemistry and biosynthesis of the nitrogenase enzyme has made the seemingly remote and for long unreachable dream more possible. In this review, we will discuss strategies how this could be accomplished using biotechnology, with a special focus on recent progress on engineering plants to express its own nitrogenase.

Comparative genomic survey of Bacillus cereus sensu stricto isolates from the dairy production chain in Brazil.

Abstract: The genomes of 262 Bacillus cereus isolates were analyzed including 69 isolates sampled from equipment, raw milk and dairy products from Brazil. The population structure of isolates showed strains belonging to known phylogenetic groups II, III, IV, V and VI. Almost all the isolates obtained from dairy products belonged to group III. Investigation of specific alleles revealed high numbers of isolates carrying toxin-associated genes including cytK (53.62%), hblA (59.42%), hblC (44.93%), hblD (53.62%), nheA (84.06%), nheB (89.86%) and nheC (84.06%) with isolates belonging to groups IV and V having significant higher prevalence of hblACD and group IV of CytK genes. Strains from dairy products had significantly lower prevalence of CytK and hblACD genes compared to isolates from equipment and raw milk/bulk tanks. Genes related to sucrose metabolism were detected at higher frequency in isolates obtained from raw milk compared to strains from equipment and utensils. The population genomic analysis demonstrated the diversity of strains and variability of putative function among B. cereus group isolates in Brazilian dairy production, with large numbers of strains potentially able to cause foodborne illness. This detailed information will contribute to targeted interventions to reduce milk contamination and spoilage associated with B. cereus in Brazil.

Climate change and One Health.

Abstract: The journal The Lancet recently published a countdown on health and climate change. Attention was focused solely on humans. However, animals, including wildlife, livestock and pets, may also be impacted by climate change. Complementary to the high relevance of awareness rising for protecting humans against climate change, here we present a One Health approach, which aims at the simultaneous protection of humans, animals and the environment from climate change impacts (climate change adaptation). We postulate that integrated approaches save human and animal lives and reduce costs when compared to public and animal health sectors working separately. A One Health approach to climate change adaptation may significantly contribute to food security with emphasis on animal source foods, extensive livestock systems, particularly ruminant livestock, environmental sanitation, and steps towards regional and global integrated syndromic surveillance and response systems. The cost of outbreaks of emerging vector-borne zoonotic pathogens may be much lower if they are detected early in the vector or in livestock rather than later in humans. Therefore, integrated community-based surveillance of zoonoses is a promising avenue to reduce health effects of climate change.

The State of The Art in Peer Review

Abstract: Scholarly communication is in a perpetual state of disruption. Within this, peer review of research articles remains an essential part of the formal publication process, distinguishing it from virtually all other modes of communication. In the last several years, there has been an explosive wave of innovation in peer review research, platforms, discussions, tools and services. This is largely coupled with the ongoing and parallel evolution of scholarly communication as it adapts to rapidly changing environments, within what is widely considered as the ‘open research’ or ‘open science’ movement. Here, we summarise the current ebb and flow around changes to peer review and consider its role in a modern digital research and communications infrastructure and suggest why uptake of new models of peer review appears to have been so low compared to what is often viewed as the ‘traditional’ method of peer review. Finally, we offer some insight into the potential futures of scholarly peer review and consider what impacts this might have on the broader scholarly research ecosystem. In particular, we focus on the key traits of certification and reputation, moderation and quality control and engagement incentives, and discuss how these interact with socio-technical aspects of peer review and academic culture.

The impact of environmental factors on carbon dioxide fixation by microalgae.

Abstract: Microalgae are among the most productive biological systems for converting sunlight into chemical energy, which is used to capture and transform inorganic carbon into biomass. The efficiency of carbon dioxide capture depends on the cultivation system configuration (photobioreactors or open systems) and can vary according to the state of the algal physiology, the chemical composition of the nutrient medium, and environmental factors such as irradiance, temperature and pH. This mini-review is focused on some of the most important environmental factors determining photosynthetic activity, carbon dioxide biofixation, cell growth rate and biomass productivity by microalgae. These include carbon dioxide and O2 concentrations, light intensity, cultivation temperature and nutrients. Finally, a review of the operation of microalgal cultivation systems outdoors is presented as an example of the impact of environmental conditions on biomass productivity and carbon dioxide fixation.

Alternative strategies for lignocellulose fermentation through lactic acid bacteria: the state of the art and perspectives.

Abstract: Lactic acid bacteria (LAB) have a long history in industrial processes as food starters and biocontrol agents, and also as producers of high-value compounds. Lactic acid, their main product, is among the most requested chemicals because of its multiple applications, including the synthesis of biodegradable plastic polymers. Moreover, LAB are attractive candidates for the production of ethanol, polyhydroalkanoates, sweeteners and exopolysaccharides. LAB generally have complex nutritional requirements. Furthermore, they cannot directly ferment inexpensive feedstocks such as lignocellulose. This significantly increases the cost of LAB fermentation and hinders its application in the production of high volumes of low-cost chemicals. Different strategies have been explored to extend LAB fermentation to lignocellulosic biomass. Fermentation of lignocellulose hydrolysates by LAB has been frequently reported and is the most mature technology. However, current economic constraints of this strategy have driven research for alternative approaches. Co-cultivation of LAB with native cellulolytic microorganisms may reduce the high cost of exogenous cellulase supplementation. Special attention is given in this review to the construction of recombinant cellulolytic LAB by metabolic engineering, which may generate strains able to directly ferment plant biomass. The state of the art of these strategies is illustrated along with perspectives of their applications to industrial second generation biorefinery processes.

Co-translational protein targeting in bacteria.

Abstract: About 30% of all bacterial proteins execute their function outside of the cytosol and have to be transported into or across the cytoplasmic membrane. Bacteria use multiple protein transport systems in parallel, but the majority of proteins engage two distinct targeting systems. One is the co-translational targeting by two universally conserved GTPases, the signal recognition particle (SRP) and its receptor FtsY, which deliver inner membrane proteins to either the SecYEG translocon or the YidC insertase for membrane insertion. The other targeting system depends on the ATPase SecA, which targets secretory proteins, i.e. periplasmic and outer membrane proteins, to SecYEG for their subsequent ATP-dependent translocation. While SRP selects its substrates already very early during their synthesis, the recognition of secretory proteins by SecA is believed to occur primarily after translation termination, i.e. post-translationally. In this review we highlight recent progress on how SRP recognizes its substrates at the ribosome and how the fidelity of the targeting reaction to SecYEG is maintained. We furthermore discuss similarities and differences in the SRP-dependent targeting to either SecYEG or YidC and summarize recent results that suggest that some membrane proteins are co-translationally targeted by SecA.

Lpp, the Braun lipoprotein, turns 50-major achievements and remaining issues.

Abstract: The discovery of Escherichia coli Lpp as the first protein with three acyl groups covalently attached to its N-terminal cysteine residue defined a new class of bacterial proteins, the lipoproteins. Lipoproteins are extracytoplasmic, globular proteins that are anchored to a membrane by a lipid moiety. Being anchored to the outer membrane, Lpp, which is also known as the Braun lipoprotein, is small (5.8 kDa) and folds into a trimeric helical structure. It is also the numerically most abundant protein in E. coli. A unique feature of Lpp is that its C-terminal lysine residue is covalently attached to the peptidoglycan, providing the only covalent connection between the outer membrane and the cell wall. Here, we review the knowledge gained on Lpp since its discovery in 1969 until the recent finding that Lpp functions as a major size determinant in the bacterial cell envelope. We also discuss the role played by Lpp in virulence and highlight the major questions that remain to be solved.

The way is the goal: how SecA transports proteins across the cytoplasmic membrane in bacteria

Abstract: In bacteria, translocation of most soluble secreted proteins (and outer membrane proteins in Gram-negative bacteria) across the cytoplasmic membrane by the Sec machinery is mediated by the essential ATPase SecA. At its core, this machinery consists of SecA and the integral membrane proteins SecYEG, which form a protein conducting channel in the membrane. Proteins are recognised by the Sec machinery by virtue of an internally encoded targeting signal, which usually takes the form of an N-terminal signal sequence. In addition, substrate proteins must be maintained in an unfolded conformation in the cytoplasm, prior to translocation, in order to be competent for translocation through SecYEG. Recognition of substrate proteins occurs via SecA-either through direct recognition by SecA or through secondary recognition by a molecular chaperone that delivers proteins to SecA. Substrate proteins are then screened for the presence of a functional signal sequence by SecYEG. Proteins with functional signal sequences are translocated across the membrane in an ATP-dependent fashion. The current research investigating each of these steps is reviewed here.

E. coli strain engineering for the production of advanced biopharmaceutical products.

Abstract: Since the emergence of the biopharmaceutical industry in the 1980's, Escherichia coli, has played an important role in the industrial production of recombinant proteins and plasmid DNA for therapeutic use. Currently, advanced biopharmaceutical products, including rationally designed recombinant proteins and viral-vector gene therapies, offer unprecedented promise for the long-term management, and even cure of disease. As such, E. coli remains an important production host for the biopharmaceutical industry. This review provides insight into the industrially relevant strain engineering approaches used to enhance both the quantity and quality of these therapeutic products.

Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools

Abstract: Pseudomonas aeruginosa is an important opportunistic pathogen, especially in the context of infections of cystic fibrosis (CF). In order to facilitate coordinated study of this pathogen, an international reference panel of P. aeruginosa isolates was assembled. Here we report the genome sequencing and analysis of 33 of these isolates and 7 reference genomes to further characterise this panel. Core genome single nucleotide variant phylogeny demonstrated that the panel strains are widely distributed amongst the P. aeruginosa population. Common loss of function mutations reported as adaptive during CF (such as in mucA and mexA) were identified amongst isolates from chronic respiratory infections. From the 40 strains analysed, 37 unique resistomes were predicted, based on the Resistance Gene Identifier method using the Comprehensive Antibiotic Resistance Database. Notably, hierarchical clustering and phylogenetic reconstructions based on the presence/absence of genomic islands (GIs), prophages and other Regions of Genome Plasticity (RGPs) supported the subdivision of P. aeruginosa into two main groups. This is the largest, most diverse analysis of GIs and associated RGPs to date, and the results suggest that, at least at the largest clade grouping level (Group 1 vs Group 2), each group may be drawing upon distinct mobile gene pools.

Metabolic engineering of Escherichia coli for the production of isoprenoids.

Abstract: Metabolic engineering is the practice of using directed genetic manipulations to rewire cellular metabolism primarily with the aim to transform the organism into a single-celled chemical factory. Using biological processes, we can produce more complex chemicals in a more sustainable way. This is particularly important for chemicals which are hard to synthesize using traditional chemistry. However, cells have evolved for growth and must be engineered to produce a single chemical at commercially viable levels. This review focuses on the strategies used to rewire cellular metabolism to produce chemicals using isoprenoid production in Escherichia coli as an example that illustrates many of the challenges faced in metabolic engineering.

The presence of colistin resistance gene mcr-1 and -3 in ESBL producing Escherichia coli isolated from food in Ho Chi Minh City, Vietnam

Abstract: Colistin is indicated for the treatment of multidrug-resistant gram-negative bacterial infections. However, the spread of colistin-resistant bacteria harbouring an mcr gene has become a serious concern. This study investigated local foods in Vietnam for contamination with colistin-resistant bacteria. A total of 261 extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli isolates from 330 meat and seafood products were analysed for colistin susceptibility and the presence of mcr genes. Approximately, 24% (62/261) of ESBL- or AmpC-producing E. coli isolates showed colistin resistance; 97% (60/62) of colistin-resistant isolates harboured mcr-1, whereas 3% (2/62) harboured mcr-3. As the result of plasmid analysis of two strains, both plasmids harbouring mcr-3 revealed that plasmid replicon type was IncFII. Sequencing analysis indicated that an insertion sequence was present near mcr-3, suggesting that IncFII plasmids harbouring mcr-3 could be transferred to other bacterial species by horizontal transfer of the plasmid or transfer with some insertion sequence. In conclusion, ESBL-producing E. coli and AmpC-producing E. coli have acquired colistin resistance because 24% of such isolates show colistin resistance and 3% of the colistin-resistant strains harbour mcr-3. We reported the present of the mcr-3-carrying ESBL-producing E. coli isolated from pork in Vietnam.

On display: autotransporter secretion and application.

Abstract: The classical monomeric autotransporters are ubiquitously used by Gram-negative bacteria to export virulence and colonization factors to their cell surface or into their surroundings. They are expressed as monomeric proteins that pass the inner and outer membrane in two consecutive steps facilitated by the Sec translocon and the Bam complex, respectively. In this mini-review we discuss how autotransporters translocate their secreted functional domains across the outer membrane. We highlight the interactions with the Bam complex and discuss how specific features of the recently solved structure of Bam lead to a mechanistic model for autotransporter secretion. Furthermore, the autotransporter secretion pathway is the system of choice for surface display of heterologous proteins for biotechnical and biomedical purposes. We summarize recent advances in the application of autotransporters with a focus on outer membrane vesicle vaccine development and discuss its limitations in secreting more complex heterologous proteins. Finally, we present an exciting new technology to circumvent secretion limitations by ligating heterologous proteins of interest to autotransporters that are displayed on the cell surface.

The functional RNA cargo of bacterial membrane vesicles.

Abstract: Bacteria secrete RNAs, some of which have effects on other cells and on other species as signalling RNAs. Prokaryotic membrane vesicles (MVs) contain a range of RNA types. The MV structure offers protection from degradation as well as receptors to facilitate delivery to target cells. Microscopic imaging and molecular biology analyses have provided evidence to demonstrate that bacterial MVs deliver their RNA into eukaryotic cells. Moreover, in some cases the RNA cargo is demonstrably functional and phenotypic changes can be identified in MV-RNA treated target cells. The challenge now is to dissect the effect of MV-RNA on target cells away from the effects of non-RNA components of the MV such as lipopolysaccharide that can co-purify with RNA.

Transport and metabolic engineering of the cell factory Corynebacterium glutamicum.

Abstract: Corynebacterium glutamicum has a long and successful history in the biotechnological production of the amino acids l-glutamate and l-lysine. In the recent years, C. glutamicum has been engineered for the production of a broad catalog of value-added compounds including organic acids, vitamins, terpenoids and proteins. Moreover, this bacterium has been engineered to realize a flexible carbon source concept enabling product formation from various second generation feedstocks without competing uses in human and animal nutrition. In this review, we highlight transport engineering to improve product export and substrate uptake or to avoid loss of intermediates by excretion as well as the application of new metabolic engineering concepts for C. glutamicum strain development including the use of designed synthetic Escherichiacoli-C. glutamicum consortia. As examples, pathway extension of l-lysine and l-glutamate biosynthesis to produce derived value-added chemicals is described. The described examples of C. glutamicum strain engineering reflect strategies to cope with the increasing complexity of biotechnological processes that are required for successful applications in the bioeconomy.

Transcriptional and environmental control of bacterial denitrification and N2O emissions.

Abstract: In oxygen-limited environments, denitrifying bacteria can switch from oxygen-dependent respiration to nitrate (NO3-) respiration in which the NO3- is sequentially reduced via nitrite (NO2-), nitric oxide (NO) and nitrous oxide (N2O) to dinitrogen (N2). However, atmospheric N2O continues to rise, a significant proportion of which is microbial in origin. This implies that the enzyme responsible for N2O reduction, nitrous oxide reductase (NosZ), does not always carry out the final step of denitrification either efficiently or in synchrony with the rest of the pathway. Despite a solid understanding of the biochemistry underpinning denitrification, there is a relatively poor understanding of how environmental signals and respective transcriptional regulators control expression of the denitrification apparatus. This minireview describes the current picture for transcriptional regulation of denitrification in the model bacterium, Paracoccus denitrificans, highlighting differences in other denitrifying bacteria where appropriate, as well as gaps in our understanding. Alongside this, the emerging role of small regulatory RNAs in regulation of denitrification is discussed. We conclude by speculating how this information, aside from providing a better understanding of the denitrification process, can be translated into development of novel greenhouse gas mitigation strategies.

Beyond nitrogen metabolism: nitric oxide, cyclic-di-GMP and bacterial biofilms.

Abstract: The nitrogen cycle pathways are responsible for the circulation of inorganic and organic N-containing molecules in nature. Among these pathways, those involving amino acids, N-oxides and in particular nitric oxide (NO) play strategic roles in the metabolism of microorganisms in natural environments and in host-pathogen interactions. Beyond their role in the N-cycle, amino acids and NO are also signalling molecules able to influence group behaviour in microorganisms and cell-cell communication in multicellular organisms, including humans. In this minireview, we summarise the role of these compounds in the homeostasis of the bacterial communities called biofilms, commonly found in environmental, industrial and medical settings. Biofilms are difficult to eradicate since they are highly resistant to antimicrobials and to the host immune system. We highlight the effect of amino acids such as glutamate, glutamine and arginine and of NO on the signalling pathways involved in the metabolism of 3',5'-cyclic diguanylic acid (c-di-GMP), a master regulator of motility, attachment and group behaviour in bacteria. The study of the metabolic routes involving these N-containing compounds represents an attractive topic to identify targets for biofilm control in both natural and medical settings.

Variable response of nirK and nirS containing denitrifier communities to long-term pH manipulation and cultivation.

Abstract: Denitrification is a key process responsible for the majority of soil nitrous oxide (N2O) emissions but the influences of pH and cultivation on the soil denitrifier community remain poorly understood. We hypothesised that the abundance and community structure of the total bacterial community and bacterial denitrifiers would be pH sensitive and that nirK and nirS containing denitrifiers would differ in their responses to change in pH and cultivation. We investigated the effect of long-term pH-adjusted soils (ranging from pH 4.2 to 6.6) under different lengths of grass cultivation (one, two and three years of ley grass) on the general bacterial and denitrifier functional communities using 16S rRNA, nirK and nirS genes as markers. Denitrifier abundance increased with pH, and at pH below 4.7 there was a greater loss in nirS abundance per unit drop in pH than soils above this threshold pH. All community structures responded to changes in soil pH, while cultivation only influenced the community structure of nirK. These differences in denitrifier responses highlight the importance of considering both nirK and nirS gene markers for estimating denitrifier activity. Identifying such thresholds in response of the microbial community to changes in pH is essential to understanding impacts of management or environmental change.

Genome mining for the search and discovery of bioactive compounds: the Streptomyces paradigm.

Abstract: The need for new antimicrobials is indisputable. The flight from natural products in drug discovery was unfortunate; however, the revolution that is genome mining, enabled by the explosion in sequencing technology, is a cause for hope. Nevertheless, renewed search and discovery is still a challenge. We explore novel metabolite diversity and the challenges in Streptomyces. Estimating the extent of novel bioactive metabolites remaining to be discovered is an important driver for future investment. Frequent re-discovery of known natural products was a major factor in big pharma exiting search and discovery, and remains a reality. We explore whether this is due to exhaustive isolation and frequent lateral gene transfer. Analysing all biosynthetic gene clusters across all genomes is challenging. Therefore, representative examples of the patterns of secondary metabolite diversity suggest that re-discovery is linked to frequent expression in frequently isolated (and frequently misidentified) strains. Lateral gene transfer of complete biosynthetic clusters is less frequent than might be perceived but frequent gene exchange implies a massive combinatorial biosynthesis experiment. Genome sequencing emphasises rare expression of many secondary metabolite gene clusters and diversification at the finest levels of phylogenetic discrimination. In addition, we are only just beginning to unravel the impact of ecology. The hidden diversity suggests that cluster cloning and heterologous expression in microbial cell factories will explore this diversity more effectively.

Redundant roles of Bradyrhizobium oligotrophicum Cu-type (NirK) and cd1-type (NirS) nitrite reductase genes under denitrifying conditions.

Abstract: Reduction of nitrite to nitric oxide gas by respiratory nitrite reductases (NiRs) is the key step of denitrification. Denitrifiers are strictly divided into two functional groups based on whether they possess the copper-containing nitrite reductase (CuNiR) encoded by nirK or the cytochrome cd1 nitrite reductase (cdNiR) encoded by nirS. Recently, some organisms carrying both nirK and nirS genes have been found. Bradyrhizobium oligotrophicum S58 is a nitrogen-fixing oligotrophic bacterium that carries a set of genes for complete denitrification of nitrate to dinitrogen, including nirK and nirS genes. We show that denitrification in S58 is functional under low-oxygen conditions (anaerobiosis and microaerobiosis), but not under aerobiosis. Under denitrifying conditions, the ΔnirK and ΔnirS single S58 mutants grew normally and their NiR activity was not affected. However, the ΔnirKS double mutant grew more slowly, presumably because the impaired NiR activity resulted in nitrite accumulation in the medium. These results suggest a redundant role for nirK and nirS genes in B. oligotrophicum S58 denitrification. In addition, we found that the nirS gene product, but not that of nirK, maintains swimming motility of S58 under aerobic and low-oxygen conditions in the presence of nitrate.

New concepts in anammox processes for wastewater nitrogen removal: recent advances and future prospects.

Abstract: The discovering of anaerobic ammonium oxidation (anammox) process led to the development of autotrophic nitrogen removal systems for the treatment of effluents with low C:N rate. The anammox processes provide an efficient way to remove high concentrations of ammonium compounds from industrial and urban wastewater and covert them to dinitrogen. Nevertheless, recently obtained results suggest new ways for research on autotrophic nitrogen removal system including possibility for low temperature operation, adaptation to high organic matter loads and antibiotics inhibition effect. For these reasons, the prevalence and spatial distribution of anammox communities in autotrophic nitrogen removal wastewater treatment technologies, as well as their role in formation of fixed biofilms, are reviewed here in order to illustrate the present and future significance of these microorganisms in environmental biotechnology.

Fixation of CO2 and CO on a diverse range of carbohydrates using anaerobic, non-photosynthetic mixotrophy.

Abstract: Biological CO2 fixation is an important technology that can assist in combating climate change. Here, we show an approach called anaerobic, non-photosynthetic mixotrophy can result in net CO2 fixation when using a reduced feedstock. This approach uses microbes called acetogens that are capable of concurrent utilization of both organic and inorganic substrates. In this study, we investigated the substrate utilization of 17 different acetogens, both mesophilic and thermophilic, on a variety of different carbohydrates and gases. Compared to most model acetogen strains, several non-model mesophilic strains displayed greater substrate flexibility, including the ability to utilize disaccharides, glycerol and an oligosaccharide, and growth rates. Three of these non-model strains (Blautia producta, Clostridium scatologenes and Thermoanaerobacter kivui) were chosen for further characterization, under a variety of conditions including H2- or syngas-fed sugar fermentations and a CO2-fed glycerol fermentation. In all cases, CO2 was fixed and carbon yields approached 100%. Finally, the model acetogen C. ljungdahlii was engineered to utilize glucose, a non-preferred sugar, while maintaining mixotrophic behavior. This work demonstrates the flexibility and robustness of anaerobic, non-photosynthetic mixotrophy as a technology to help reduce CO2 emissions.

Non-conventional yeast cell factories for sustainable bioprocesses.

Abstract: The non-conventional yeasts Kluyveromyces lactis, Yarrowia lipolytica, Ogataea polymorpha and Pichia pastoris have been developed as eukaryotic expression hosts because of their desirable growth characteristics, including inhibitor and thermo-tolerance, utilisation of diverse carbon substrates and high amount of extracellular protein secretion. These yeasts already have established in the heterologous production of vaccines, therapeutic proteins, food additives and bio-renewable chemicals, but recent advances in the genetic tool box have the potential to greatly expand and diversify their impact on biotechnology. The diversity of these yeasts includes many strains possessing highly useful, and in some cases even uncommon, metabolic capabilities potentially helpful for the bioprocess industry. This review outlines the recent updates of non-conventional yeast in sustainable bioprocesses.

The colors of biotechnology: general overview and developments of white, green and blue areas.

Abstract: Biotechnology is responsible for the manipulation of living organisms or their components for the production of products that are of benefit to human kind. Due to the wide range of applications, colors have been used to differentiate the main areas of research, such as white (industrial), green (agricultural) and blue (marine and fresh-water), among others. Thus, this review outlines the impacts of these areas of biotechnology, emphasizing their impact and potential to replace carbon-based technologies with more sustainable technologies.