Organo-mineral imprints in fossil cyanobacterial mats of an Antarctic lake

peer reviewe

Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts

IntroductionIt has been recognized that capripoxvirus infections have a strong cutaneous tropism with the manifestation of skin lesions in the form of nodules and scabs in the respective hosts, followed by necrosis and sloughing off. Considering that the skin microbiota is a complex community of commensal bacteria, fungi and viruses that are influenced by infections leading to pathological states, there is no evidence on how the skin microbiome is affected during capripoxvirus pathogenesis.MethodsIn this study, shotgun metagenomic sequencing was used to investigate the microbiome in pox lesions from hosts infected with lumpy skin disease virus and sheep pox virus.ResultsThe analysis revealed a high degree of variability in bacterial community structures across affected skin samples, indicating the importance of specific commensal microorganisms colonizing individual hosts. The most common and abundant bacteria found in scab samples were Fusobacterium necrophorum, Streptococcus dysgalactiae, Helcococcus ovis and Trueperella pyogenes, irrespective of host. Bacterial reads belonging to the genera Moraxella, Mannheimia, Corynebacterium, Staphylococcus and Micrococcus were identified.DiscussionThis study is the first to investigate capripox virus-associated changes in the skin microbiome using whole-genome metagenomic profiling. The findings will provide a basis for further investigation into capripoxvirus pathogenesis. In addition, this study highlights the challenge of selecting an optimal bioinformatics approach for the analysis of metagenomic data in clinical and veterinary practice. For example, direct classification of reads using a kmer-based algorithm resulted in a significant number of systematic false positives, which may be attributed to the peculiarities of the algorithm and database selection. On the contrary, the process of de novo assembly requires a large number of target reads from the symbiotic microbial community. In this work, the obtained sequencing data were processed by three different approaches, including direct classification of reads based on k-mers, mapping of reads to a marker gene database, and de novo assembly and binning of metagenomic contigs. The advantages and disadvantages of these techniques and their practicality in veterinary settings are discussed in relation to the results obtained

Algal Bloom Occurrence and Effects in Russia

Eutrophication caused by the entry of nutrients into a water body may lead to algal bloom. Russia possesses the world’s second highest supply of renewable freshwater resources and has faced the problem of eutrophication for many years. Nevertheless, as far as we know, no general analysis of Russia’s algal bloom situation has been before carried out. We have analyzed mass media and scientific reports about algal outbreaks from 2016 to 2018, which allowed us to determine the geographical distribution of algal blooms in Russia, as well as the major effects of eutrophication. As a result, we showed that algal blooms happened in all major climate zones and all federal districts. Cyanobacteria are the most frequently reported photosynthetic organisms comprising algal blooms in freshwater reservoirs located in the continental part of Russia and in the Baltic Sea. Dinoflagellate dominated blooms are more characteristic for the coastal parts of the northeastern Pacific Ocean. The largest number of reports comes from the south of the European part of Russia. However, we did not find significant correlations between state statistics data on factors possibly affecting eutrophication (e.g., population, arable land area, fertilizers, livestock, air temperature, etc.) and the number of algal outbreaks in the regions. Mass media analysis showed that algal blooms attract considerable public attention in Russia, which requires the scientific community to actively participate in solving the problem

Cyanobacterial diversity in soil crusts in the Sör Rondane Mountains

Antarctica is the only continent that is dominated by microbial (cyanobacteria and algae) and lower plant (predominantly mosses and lichens) communities. Cyanobacteria are photosynthetic bacteria that require solar light, liquid water, air and some mineral nutrients for growth. They serve as primary producers of organic matter in Antarctic ecosystems providing energy to other physiological groups of microorganisms and invertebrates. Cyanobacteria form macroscopically visible crusts or thin biofilms on the surface of soils and rocks, or occupy endolithic niches in Antarctic mountains. Mountains exposed above the ice sheet could have remained ice-free during glaciation maxima in Antarctica. They could serve as a refuge for terrestrial biodiversity and potential source for recolonization of surrounding habitats during glacier retreat. Cyanobacterial diversity in habitats located above 1 km a.s.l. was studied in several Antarctic locations. These include: the Vinson Massif in Ellsworth Mountains (2000-2500 m a.s.l.), Beacon (1176 m a.s.l.) and University Valleys (1700 m a.s.l.) in the "stable upland zone" of the McMurdo Dry Valleys (Southern Victoria Land) and the Sör Rondane Mountains (1370-1700 m a.s.l.) (Yergeau et al., 2007; Wood et al., 2008; Fernandez-Carazo et al., 2012). The goal of our work was to study cyanobacterial diversity of cyanobacteria in the Sör Rondane Mountains in the vicinity of Belgian Princess Elisabeth Station. Previous estimates of the diversity showed the presence of 10 morphotypes and 13 OTUs of cyanobacteria in 10 samples of biofilms and microbial crusts (Fernandez-Carazo et al., 2012). We performed a broader sampling and studied cyanobacterial diversity using DGGE with cyanospecific primers and microscopy. In 126 samples, we observed 15 morphotypes of cyanobacteria. 28 representative samples were selected for molecular analyses that revealed the presence of 28 OTUs (groups of 16S rRNA sequences sharing at least 97,5% sequence similarity). Comparison with other mountainous areas of Antarctica showed that the Sör Rondane Mountains harbor a significantly higher cyanobacterial diversity. Molecular analysis of the cyanobacterial diversity in Beacon Valley didn't show the presence of cyanobacteria (Wood et al., 2008), though a strain of Chroococcidiopsis sp. (CCMEE 134) was isolated from a sample collected there (Billi et al., 2011). A strain of Chroococcidiopsis sp. (CCMEE 171-A789-2) was also isolated from samples collected in University Valley (Cumbers & Rothschild, 2014). 5 OTUs of cyanobacteria were detected in samples collected in Ellsworth Mountains despite of the presumably harsher climate (78°31′S latitude compared to 77°49′S for Beacon Valley) and higher altitude (Yergeau et al., 2007). No reliable climate data are available for the discussed areas, except for the Sor Rondane Mountains. We propose that the higher diversity of cyanobacteria detected near the Princess Elisabeth Station could be explained by a more intensive sampling or by a more northern location of the area (72°0′S).BELDIV

Diversité des communautés cyanobactériennes des Montagnes Sor Rondane

The new Belgian “Princess Elisabeth” research station was built in 2009 and is located 200 km inland in the Western part of the Sør Rondane Mountains (Eastern Antarctica). The BELSPO projects ANTAR-IMPACT and BELDIVA aimed to evaluate the diversity and the distribution patterns of the microorganisms from different types of habitats in a radius of 50 km around the Belgian station. These data will serve to follow future anthropogenic and climatic impacts on these communities. Here, we focus on the diversity of cyanobacteria.BELDIV

Simulation du Changement climatique en Antarctique continental utilisant les Open Top Chambers

In continental Antarctica, the environnmental conditions are extreme and only microbial organisms can withstand them. Currently, the majority of OTCs experiments are being held in Maritime Antarctica but it would be interesting to have such data for the continental part of Eastern Antarctica. To monitor the response of the microbial communities to local simulations of climate change, 8 Open-Top Chambers (OTC) were installed close to the Princess Elisabeth station, in the Sor Rondane Mountains in January 2010. They are located on the Utsteinen ridge, the Tanngarden granite outcrop, the Teltet nunatak and the fourth nunatak of the Pingvinane range. In each location, two OTCs and a control area were established. Temperature and humidity loggers were installed inside the OTCs and outside, in the control areas, to estimate the environmental changes induced by the OTCs.BELDIV

Les cyanobactéries habitant les croutes biotiques d'un désert polaire

Molecular and morphological methods were applied to study cyanobacterial community composition in biological soil crusts (BSCs) from four areas (two nunataks and two ridges) in the Sør Rondane Mountains, Antarctica. The sampling sites serve as control areas for open top chambers (OTCs) which were placed in 2010 at the time of sample collection and will be compared with BSC samples taken from the OTCs in future. Cyanobacterial cell biovolume was estimated using epifluorescence microscopy, which revealed the dominance of filamentous cyanobacteria in all studied sites except the Utsteinen ridge, where unicellular cyanobacteria were the most abundant. Cyanobacterial diversity was studied by a combination of molecular fingerprinting methods based on the 16S rRNA gene (denaturing gradient gel electrophoresis (DGGE) and 454 pyrosequencing) using cyanobacteria specific primers. The number of DGGE sequences obtained per site was variable and, therefore, a high-throughput method was later employed to improve the diversity coverage. Consistent with previous surveys in Antarctica, both methods showed that filamentous cyanobacteria such as Leptolyngbya sp., Phormidium sp. and Microcoleus sp. were dominant in the studied sites. In addition, the studied localities differed in substrate type, climatic conditions and soil parameters, which likely resulted in differences in cyanobacterial community composition. Furthermore, the BSC growing on gneiss pebbles had lower cyanobacterial abundances than BSCs associated to granitic substrates.BELDIV

Biodiversity studies in Open-Top Chambers in continental Antarctica

Open Top Chambers are passive warming systems used to experimentally assess the effect of climate change on terrestrial ecosystems, and they were used in several Antarctic regions to study the response of biotic communities. In the BELSPO BELDIVA project, OTCs were used in continental Eastern Antarctica, where environmental conditions are very extreme. In January 2010, 8 Open-Top Chambers (OTC) were installed in four ice-free regions of the Sör Rondane Mountains, namely on the Utsteinen ridge, the Tanngarden granite outcrop, the Teltet nunatak and the fourth nunatak of the Pingvinane range.ANTAR-IMPACT, BELDIV

AlgalTextile - a new biohybrid material for wastewater treatment

Efficient nutrient extraction from wastewater and reuse as bio-fertilizer is an important task for reducing anthropogenic load toward circular economy. Inspired by microbial mats and biofilms, we developed a new material AlgalTextile (AT) that effectively absorbs nutrients from a medium. AT consists of three fully organic components: microalgae, alginate and textile. AT sequestered up to 99% of phosphorus (P-PO4) and 76% of total bound nitrogen from a medium. The uptake rate of phosphorus and nitrogen by AT was highest among all methods using photosynthetic microorganisms, but lower than EBPR and physicochemical methods for phosphorus removal, and anammox and denitrifying bacteria for nitrogen removal. Advantages of AT are its easy production, possibility of seasonal use and utilization as fertilizer. AT as biofertilizer for cress resulted in 35% greater length compared to the control. This outlines a promising technique for seasonal wastewater treatment, improving soil fertility and treatment of polluted surface runoff