Diazotrophic microbial community of coastal microbial mats of the southern North Sea

The diazotrophic community in microbial mats growing along the shore of the North Sea barrier island Schiermonnikoog (The Netherlands) was studied using microscopy, lipid biomarkers, stable carbon (δ(13) C(TOC) ) and nitrogen (δ(15) N) isotopes as well as by constructing and analyzing 16S rRNA gene libraries. Depending on their position on the littoral gradient, two types of mats were identified, which showed distinct differences regarding the structure, development and composition of the microbial community. Intertidal microbial mats showed a low species diversity with filamentous non-heterocystous Cyanobacteria providing the main mat structure. In contrast, supratidal microbial mats showed a distinct vertical zonation and a high degree of species diversity. Morphotypes of non-heterocystous Cyanobacteria were recognized as the main structural component in these mats. In addition, unicellular Cyanobacteria were frequently observed, whereas filamentous heterocystous Cyanobacteria occurred only in low numbers. Besides the apparent visual dominance of cyanobacterial morphotpyes, 16S rRNA gene libraries indicated that both microbial mat types also included members of the Proteobacteria and the Cytophaga-Flavobacterium-Bacteroides group as well as diatoms. Bulk δ(15) N isotopes of the microbial mats ranged from +6.1‰ in the lower intertidal to -1.2‰ in the supratidal zone, indicating a shift from predominantly nitrate utilization to nitrogen fixation along the littoral gradient. This conclusion was supported by the presence of heterocyst glycolipids, representing lipid biomarkers for nitrogen-fixing heterocystous Cyanobacteria, in supratidal but not in intertidal microbial mats. The availability of combined nitrogen species might thus be a key factor in controlling and regulating the distribution of the diazotrophic microbial community of Schiermonnikoog.     

Analysis of the microbial community of the biocathode of a hydrogen-producing microbial electrolysis cell

The microbial electrolysis cell (MEC) is a promising system for hydrogen production. Still, expensive catalysts such as platinum are needed for efficient hydrogen evolution at the cathode. Recently, the possibility to use a biocathode as an alternative for platinum was shown. The microorganisms involved in hydrogen evolution in such systems are not yet identified. We analyzed the microbial community of a mixed culture biocathode that was enriched in an MEC bioanode. This biocathode produced 1.1 A m⁻² and 0.63 m³ H₂ m⁻³ cathode liquid volume per day. The bacterial population consisted of 46% Proteobacteria, 25% Firmicutes, 17% Bacteroidetes, and 12% related to other phyla. The dominant ribotype belonged to the species Desulfovibrio vulgaris. The second major ribotype cluster constituted a novel taxonomic group at the genus level, clustering within uncultured Firmicutes. The third cluster belonged to uncultured Bacteroidetes and grouped in a taxonomic group from which only clones were described before; most of these clones originated from soil samples. The identified novel taxonomic groups developed under environmentally unusual conditions, and this may point to properties that have not been considered before. A pure culture of Desulfovibrio strain G11 inoculated in a cathode of an MEC led to a current development from 0.17 to 0.76 A m⁻² in 9 days, and hydrogen gas formation was observed. On the basis of the known characteristics of Desulfovibrio spp., including its ability to produce hydrogen, we propose a mechanism for hydrogen evolution through Desulfovibrio spp. in a biocathode system.     

Analysis of the microbial proteome

Proteomics has begun to provide insight into the biology of microorganisms. The combination of proteomics with genetics, molecular biology, protein biochemistry and biophysics is particularly powerful, resulting in novel methods to analyse complex protein mixtures. Emerging proteomic technologies promise to increase the throughput of protein identifications from complex mixtures and allow for the quantification of protein expression levels.     

Salting-in the microbial cytoplasm

Microbial organisms are known to rely for osmotic regulatory purposes on an assortment of low molecular weight molecules earmarked for function as osmolytes. The so-called 'compatible' subclass of osmolyte, notably glycine betaine, is distinguished by a propensity to avoid the large bound fraction of cytoplasmic water adsorbed at the surface of biological macromolecules. Here we argue that this property is implicated in thermodynamic stabilisation of the cytoplasm. A rudimentary molecular statistical approach indicates that flooding the cytoplasm with large amounts of compatible osmolyte is an effective way to deal with the threat of phase separation.     

Changes in the microbial community during repeated anaerobic microbial dechlorination of pentachlorophenol

Pentachlorophenol (PCP) has been widely used as a pesticide in paddy fields and has imposed negative ecological effect on agricultural soil systems, which are in typically anaerobic conditions. In this study, we investigated the effect of repeated additions of PCP to paddy soil on the microbial communities under anoxic conditions. Acetate was added as the carbon source to induce and accelerate cycles of the PCP degradation. A maximum degradation rate occurred at the 11th cycle, which completely transformed 32.3 μM (8.6 mg L^?1) PCP in 5 days. Illumina high throughput sequencing of 16S rRNA gene was used to profile the diversity and abundance of microbial communities at each interval and the results showed that the phyla of Bacteroidates, Firmicutes, Proteobacteria, and Euryarchaeota had a dominant presence in the PCP-dechlorinating cultures. Methanosarcina, Syntrophobotulus, Anaeromusa, Zoogloea, Treponema, W22 (family of Cloacamonaceae), and unclassified Cloacamonales were found to be the dominant genera during PCP dechlorination with acetate. The microbial community structure became relatively stable as cycles increased. Treponema, W22, and unclassified Cloacamonales were firstly observed to be associated with PCP dechlorination in the present study. Methanosarcina that have been isolated or identified in PCP dechlorination cultures previously was apparently enriched in the PCP dechlorination cultures. Additionally, the iron-cycling bacteria Syntrophobotulus, Anaeromusa, and Zoogloea were enriched in the PCP dechlorination cultures indicated they were likely to play an important role in PCP dechlorination. These findings increase our understanding for the microbial and geochemical interactions inherent in the transformation of organic contaminants from iron rich soil, and further extend our knowledge of the PCP-transforming microbial communities in anaerobic soil conditions.     

Exploring the diversity of the microbial world

Yale's Microbial Diversity Institute (MDI) comprises scientists who seek to understand the largely unknown microbial world. In the first MDI symposium at Yale's West Campus in October 2010, four speakers discussed their research in diverse fields within the microbial sciences. The highlights of the symposium are presented here along with an outlook on the future of the MDI.     

Repositioning microbial biotechnology against COVID-19: the case of microbial production of flavonoids

Coronavirus-related disease 2019 (COVID-19) became a pandemic in February 2020, and worldwide researchers try to tackle the disease with approved drugs of all kinds, or to develop novel compounds inhibiting viral spreading. Flavonoids, already investigated as antivirals in general, also might bear activities specific for the viral agent causing COVID-19, SARS-CoV-2. Microbial biotechnology and especially synthetic biology may help to produce flavonoids, which are exclusive plant secondary metabolites, at a larger scale or indeed to find novel pharmaceutically active flavonoids. Here, we review the state of the art in (i) antiviral activity of flavonoids specific for coronaviruses and (ii) results derived from computational studies, mostly docking studies mainly inhibiting specific coronaviral proteins such as the 3CL (main) protease, the spike protein or the RNA-dependent RNA polymerase. In the end, we strive towards a synthetic biology pipeline making the fast and tailored production of valuable antiviral flavonoids possible by applying the last concepts of division of labour through co-cultivation/microbial community approaches to the DBTL (Design, Build, Test, Learn) principle.     

Significance of microbial interactions in control of microbial ecosystems

A microbial ecosystem represents a delicately balanced population of microorganisms each interacting with and influencing the other members of the population. An understanding of the nature and effects of these interactions is essential to improving the performance of these ecologies, which are important, in such diverse processes as biological waste treatment procedures, water pollution abatement, industrial fermentations, human or animal digestives processes and in soil. There are several types of mocrobial interactions, such as commensalism, inhibition, food competition, predation, parasitism, and synergism, which either singly or in combination may influence the functioning of the microbial ecology. To understand interactions, it is necessary to perform a detailed study of the physiology of the individual predominating microorganisms to establish their requirements with respect to such environmental factors as nutrients, temperature, pH, oxidation-reduction potential, removal of waste products, or toxic materials which may be involved in control processes and to determine how these factors affect their capabilities. The sum total of this information will indicate the possible interactions between the microorganisms and will form the basis for conducting experiments either in the laboratory or with mathematical models. Such experiments will lead to an understanding of microbial activities and to the formulation of control measures, often using an alteration of the environmental factors for regulation of the microbial ecologies. Extensive research remains to be done on the microbial interact inns in obtain the desired, precise control of these ecological processes.     

Status of the microbial census.

Over the past 20 years, more than 78,000 16S rRNA gene sequences have been deposited in GenBank and the Ribosomal Database Project, making the 16S rRNA gene the most widely studied gene for reconstructing bacterial phylogeny. While there is a general appreciation that these sequences are largely unique and derived from diverse species of bacteria, there has not been a quantitative attempt to describe the extent of sequencing efforts to date. We constructed rarefaction curves for each bacterial phylum and for the entire bacterial domain to assess the current state of sampling and the relative taxonomic richness of each phylum. This analysis quantifies the general sense among microbiologists that we are a long way from a complete census of the bacteria on Earth. Moreover, the analysis indicates that current sampling strategies might not be the most effective ones to describe novel diversity because there remain numerous phyla that are globally distributed yet poorly sampled. Based on the current level of sampling, it is not possible to estimate the total number of bacterial species on Earth, but the minimum species richness is 35,498. Considering previous global species richness estimates of 10(7) to 10(9), we are certain that this estimate will increase with additional sequencing efforts. The data support previous calls for extensive surveys of multiple chemically disparate environments and of specific phylogenetic groups to advance the census most rapidly.     

Adaptive response of microbial communities to soluble microbial products

We carried out two experiments to study the influence of soluble microbial products (SMP) on biomass concentration [defined as mixed liquor suspended solids (MLSS)] and removal of soluble biological and chemical oxygen demands (sBOD₅ and sCOD): (1) SMP were allowed to accumulate, and (2) SMP content was artificially reduced by washing the biomass. The daily initial sCOD in both experiments was kept constant at 859±6 mg/l for 16 days. In experiment 1, the highest sCOD removal (80%) occurred during the first day. Thereafter, it decreased successively to 40% [sludge retention time (SRT), 12 days], after which it increased steadily to 50±4%. Variations in residual sCOD were accompanied by variations in sBOD₅, showing that the biodegradability of the accumulated SMP components was changing. MLSS fluctuated within the range 1,200±25–1,993±58 mg/l. We attributed the irregular accumulation of the biomass to variations in the biodegradability of SMP components. The initial sBOD₅/MLSS ratio varied according to variations in initial sBOD₅ and MLSS, whereas the residual ratio was constant at 0.025±0.008. This indicated a direct relationship between the concentrations of biomass and SMP produced. In experiment 2, MLSS increased from 1,200±25 to a constant value (2,810±16 mg/l; SRT, 12 days). After this time, no decrease or increase in MLSS was observed. Correspondingly, sCOD and sBOD₅ removal increased from 80–97 to 84–99%. A stable microbial community that could consume organic matter efficiently was developed under these conditions.     

Harnessing the power of microbial metabolism

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Exploitation of the electro-optical characteristics of microbial suspensions for determining p-nitrophenol and microbial degradative activity

The effect of p-nitrophenol metabolism on the electrophysical properties of a microbial cell suspension of Acinetobacter calcoaceticum was investigated. The dependence of the suspension's optical density changes due to the orientation of the electric field on the frequency of an orienting electric field (orientational spectra) over the range 10–10 000 kHz was used. Upon optimization of cell culture conditions, followed by orientational spectrum measurements, it was found that the most dramatic changes in orientation spectrum associated with p-nitrophenol metabolism took place over the frequency range 10–1000 kHz. Additionally, a linear dependence of the magnitude of the electrooptical effect on p-nitrophenol concentrations of 0.1–0.8 mM was established. The minimum p-nitrophenol concentration detectable by this calibration was 0.1 mM.     

The influence of soluble microbial products on microbial community composition: hypothesis of microbial community succession

Soluble microbial products (SMP) are organic compounds produced by activated sludge microorganisms as they degrade substrates. They include by-products of microbial activity, death and lysis. The available literature does not reveal how SMP influence microbial community composition. In this regard, we microscopically studied changes in composition of microbial communities, especially protozoa and metazoa, under the influence of increased as well as reduced levels of SMP. The presence of SMP at high level significantly caused changes in microbial community composition. Microbial species shifted from attached ciliates (12-175 microm) to free-swimming and crawling ciliates (35-330 microm) and then invertebrates, which included rotifers (0.2-1 mm) and nematodes (1-50 mm). The shift of small-size microorganisms to large ones was observed as one of the most significant influences of SMP. Attached ciliates reappeared when we removed the SMP that had accumulated in the bioreactors - we have called this as the resurrection phenomenon of microorganisms. Such rapid changes in microbial community composition were not observed in the experiment with low concentration of SMP. Overall, the results suggest that accumulation of SMP is one of the intrinsic regulatory mechanisms that control viability and dormancy of microbial communities in activated sludge.     

High shear enrichment improves the performance of the anodophilic microbial consortium in a microbial fuel cell

In many microbial bioreactors, high shear rates result in strong attachment of microbes and dense biofilms. In this study, high shear rates were applied to enrich an anodophilic microbial consortium in a microbial fuel cell (MFC). Enrichment at a shear rate of about 120 s^?1 resulted in the production of a current and power output two to three times higher than those in the case of low shear rates (around 0.3 s^?1). Biomass and biofilm analyses showed that the anodic biofilm from the MFC enriched under high shear rate conditions, in comparison with that under low shear rate conditions, had a doubled average thickness and the biomass density increased with a factor 5. The microbial community of the former, as analysed by DGGE, was significantly different from that of the latter. The results showed that enrichment by applying high shear rates in an MFC can result in a specific electrochemically active biofilm that is thicker and denser and attaches better, and hence has a better performance.