Bacterial strains of the genus Sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (PAH) as the sole source of carbon and energy. The ...direct detection of Sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. In this study, a culture-independent PCR-based detection method using specific primers targeting the Sphingomonas 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) was developed to assess Sphingomonas diversity in PAH-contaminated soils. PCR using the new primer pair on a set of template DNAs of different bacterial genera showed that the method was selective for bacteria belonging to the family Sphingomonadaceae. Single-band DGGE profiles were obtained for most Sphingomonas strains tested. Strains belonging to the same species had identical DGGE fingerprints, and in most cases, these fingerprints were typical for one species. Inoculated strains could be detected at a cell concentration of 10(4) CFU g of soil-1. The analysis of Sphingomonas population structures of several PAH-contaminated soils by the new PCR-DGGE method revealed that soils containing the highest phenanthrene concentrations showed the lowest Sphingomonas diversity. Sequence analysis of cloned PCR products amplified from soil DNA revealed new 16S rRNA gene Sphingomonas sequences significantly different from sequences from known cultivated isolates (i.e., sequences from environmental clones grouped phylogenetically with other environmental clone sequences available on the web and that possibly originated from several potential new species). In conclusion, the newly designed Sphingomonas-specific PCR-DGGE detection technique successfully analyzed the Sphingomonas communities from polluted soils at the species level and revealed different Sphingomonas members not previously detected by culture-dependent detection techniques.
To enable long-distance space travel, the development of a highly efficient and robust system to recover nutrients from waste streams is imperative. The inability of the current physicochemical-based ...environmental control and life support system (ECLSS) on the ISS to produce food
in situ
and to recover water and oxygen at high enough efficiencies results in the need for frequent resupply missions from Earth. Therefore, alternative strategies like biologically-based technologies called bioregenerative life support systems (BLSSs) are in development. These systems aim to combine biological and physicochemical processes, which enable
in situ
water, oxygen, and food production (through the highly efficient recovery of minerals from waste streams). Hence, minimalizing the need for external consumables. One of the BLSS initiatives is the European Space Agency’s (ESA) Micro-Ecological Life Support System Alternative (MELiSSA). It has been designed as a five-compartment bioengineered system able to produce fresh food and oxygen and to recycle water. As such, it could sustain the needs of a human crew for long-term space exploration missions. A prerequisite for the self-sufficient nature of MELiSSA is the highly efficient recovery of valuable minerals from waste streams. The produced nutrients can be used as a fertilizer for food production. In this review, we discuss the need to shift from the ECLSS to a BLSS, provide a summary of past and current BLSS programs and their unique approaches to nitrogen recovery and processing of urine waste streams. In addition, compartment III of the MELiSSA loop, which is responsible for nitrogen recovery, is reviewed in-depth. Finally, past, current, and future related ground and space demonstration and the space-related challenges for this technology are considered.
There are still many challenges to overcome for human space exploration beyond low Earth orbit (LEO) (e.g., to the Moon) and for long-term missions (e.g., to Mars). One of the biggest problems is the ...reliable air, water and food supply for the crew. Bioregenerative life support systems (BLSS) aim to overcome these challenges using bioreactors for waste treatment, air and water revitalization as well as food production. In this review we focus on the microbial photosynthetic bioprocess and photobioreactors in space, which allow removal of toxic carbon dioxide (CO
) and production of oxygen (O
) and edible biomass. This paper gives an overview of the conducted space experiments in LEO with photobioreactors and the precursor work (on ground and in space) for BLSS projects over the last 30 years. We discuss the different hardware approaches as well as the organisms tested for these bioreactors. Even though a lot of experiments showed successful biological air revitalization on ground, the transfer to the space environment is far from trivial. For example, gas-liquid transfer phenomena are different under microgravity conditions which inevitably can affect the cultivation process and the oxygen production. In this review, we also highlight the missing expertise in this research field to pave the way for future space photobioreactor development and we point to future experiments needed to master the challenge of a fully functional BLSS.
Many bacteria in the environment have adapted to the presence of toxic heavy metals. Over the last 30 years, this heavy metal tolerance was the subject of extensive research. The bacterium ...Cupriavidus metallidurans strain CH34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction. We present here the full genome sequence of strain CH34 and the manual annotation of all its genes. The genome of C. metallidurans CH34 is composed of two large circular chromosomes CHR1 and CHR2 of, respectively, 3,928,089 bp and 2,580,084 bp, and two megaplasmids pMOL28 and pMOL30 of, respectively, 171,459 bp and 233,720 bp in size. At least 25 loci for heavy-metal resistance (HMR) are distributed over the four replicons. Approximately 67% of the 6,717 coding sequences (CDSs) present in the CH34 genome could be assigned a putative function, and 9.1% (611 genes) appear to be unique to this strain. One out of five proteins is associated with either transport or transcription while the relay of environmental stimuli is governed by more than 600 signal transduction systems. The CH34 genome is most similar to the genomes of other Cupriavidus strains by correspondence between the respective CHR1 replicons but also displays similarity to the genomes of more distantly related species as a result of gene transfer and through the presence of large genomic islands. The presence of at least 57 IS elements and 19 transposons and the ability to take in and express foreign genes indicates a very dynamic and complex genome shaped by evolutionary forces. The genome data show that C. metallidurans CH34 is particularly well equipped to live in extreme conditions and anthropogenic environments that are rich in metals.
The space environment is extreme for plants growth and survival as gravity (gravitropism modification, water distribution), radiations (mutations enhancers), light spectrum regime and temperature are ...not optimal. Photosynthetic microorganisms are a foreseen solution for supporting plant development, growth, and stress tolerance in closed environments, like those designed for space colonisation. Indeed, photosynthetic microorganisms are known as secondary metabolites producers (exopolysaccharides, indole alkaloids, fertilisers) able to impact plant stimulation. Studying their abilities, application methodologies and best strains for space agriculture may lead to developing a sustainable and efficient approach for food production. Furthermore, as these microorganisms could also be used to produce oxygen and recycle waste materials increasing their interest in closed loop systems is undeniable. In this review we provide an overview of the current state of knowledge about existing biostimulants, their effects and applications, and the potential brought by photosynthetic microorganisms for life in closed environments.
Highlights
Cyanobacteria's and microalgae's secondary metabolites can act as biostimulants for vascular plants when applied to the roots or the leaves.
Production of secondary metabolites in cyanobacteria can be enhanced in stressful environments.
Cyanobacteria can survive space-like stress by sur-producing secondary metabolites giving an advantage for space farming as a source of biostimulant compounds.
Abstract
Microorganisms are employed to mine economically important elements from rocks, including the rare earth elements (REEs), used in electronic industries and alloy production. We carried out a ...mining experiment on the International Space Station to test hypotheses on the bioleaching of REEs from basaltic rock in microgravity and simulated Mars and Earth gravities using three microorganisms and a purposely designed biomining reactor.
Sphingomonas desiccabilis
enhanced mean leached concentrations of REEs compared to non-biological controls in all gravity conditions. No significant difference in final yields was observed between gravity conditions, showing the efficacy of the process under different gravity regimens.
Bacillus subtilis
exhibited a reduction in bioleaching efficacy and
Cupriavidus metallidurans
showed no difference compared to non-biological controls, showing the microbial specificity of the process, as on Earth. These data demonstrate the potential for space biomining and the principles of a reactor to advance human industry and mining beyond Earth.
In ecological studies, microbial diversity is nowadays mostly assessed via the detection of phylogenetic marker genes, such as 16S rRNA. However, PCR amplification of these marker genes produces a ...significant amount of artificial sequences, often referred to as chimeras. Different algorithms have been developed to remove these chimeras, but efforts to combine different methodologies are limited. Therefore, two machine learning classifiers (reference-based and de novo CATCh) were developed by integrating the output of existing chimera detection tools into a new, more powerful method. When comparing our classifiers with existing tools in either the reference-based or de novo mode, a higher performance of our ensemble method was observed on a wide range of sequencing data, including simulated, 454 pyrosequencing, and Illumina MiSeq data sets. Since our algorithm combines the advantages of different individual chimera detection tools, our approach produces more robust results when challenged with chimeric sequences having a low parent divergence, short length of the chimeric range, and various numbers of parents. Additionally, it could be shown that integrating CATCh in the preprocessing pipeline has a beneficial effect on the quality of the clustering in operational taxonomic units.
Abstract
The development of high-throughput sequencing technologies has revolutionised the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon ...sequencing reads into operational taxonomic units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for bacterial species. Our results show that the robustness of such a generalised cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene. It will lead to biases in diversity metrics and makes it hard to compare results obtained with amplicons derived with different primer sets. The method introduced within this work takes into account the differential evolutional rates of taxonomic lineages in order to define a dynamic and taxonomic-dependent OTU clustering cut-off score. For a taxonomic family consisting of species showing high evolutionary conservation in the amplified variable regions, the cut-off will be more stringent than 97%. By taking into consideration the amplified variable regions and the taxonomic family when defining this cut-off, such a threshold will lead to more robust results and closer correspondence between OTUs and species. This approach has been implemented in a publicly available software package called DynamiC.
More accurate and robust estimates of microbial diversity are generated when performing an OTU clustering step using a dynamic cut-off that integrates bacterial taxonomy and differential evolutionary rates.
Abstract
The Boom Clay in Belgium is investigated in the context of geological nuclear waste disposal, making use of the High Activity Disposal Experimental Site (HADES) underground research ...facility. This facility, located in the Boom Clay at a depth of 225 m below the surface, offers a unique access to a microbial community in an environment, of which all geological and geochemical characteristics are being thoroughly studied. This study presents the first elaborate description of a microbial community in water samples retrieved from a Boom Clay piezometer (borehole water). Using an integrated approach of microscopy, metagenomics, activity screening and cultivation, the presence and activity of this community are disclosed. Despite the presumed low-energy environment, microscopy and molecular analyses show a large bacterial diversity and richness, tending to correlate positively with the organic matter content of the environment. Among 10 borehole water samples, a core bacterial community comprising seven bacterial phyla is defined, including both aerobic and anaerobic genera with a range of metabolic preferences. In addition, a corresponding large fraction of this community is found cultivable and active. In conclusion, this study shows the possibility of a microbial community of relative complexity to persist in subsurface Boom Clay borehole water.
Environmental uranium pollution due to industries producing naturally occurring radioactive material or nuclear accidents and releases is a global concern. Uranium is hazardous for ecosystems as well ...as for humans when accumulated through the food chain, through contaminated groundwater and potable water sources, or through inhalation. In particular, uranium pollution pressures microbial communities, which are essential for healthy ecosystems. In turn, microorganisms can influence the mobility and toxicity of uranium through processes like biosorption, bioreduction, biomineralization, and bioaccumulation. These processes were characterized by studying the interaction of different bacteria with uranium. However, most studies unraveling the underlying molecular mechanisms originate from the last decade. Molecular mechanisms help to understand how bacteria interact with radionuclides in the environment. Furthermore, knowledge on these underlying mechanisms could be exploited to improve bioremediation technologies. Here, we review the current knowledge on bacterial uranium resistance and how this could be used for bioremediation applications.
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