Microbiome Changes of Endemic Lake Baikal Sponges during Bleaching Syndrome Development

The sponge (Porifera) microbiome is an indicator of both natural and anthropogenic stressors. Studying Baikal sponge microbial communities could help reveal if there is a connection between bacterial symbionts and a mass sponge bleaching event that was recently detected; 16S rRNA sequencing was performed among healthy and diseased freshwater sponges of Lubomirskia baikalensis and Baikalospongia intermedia, which were collected from Lake Baikal, Russia. A phylum-based taxonomic classification showed that Chlorophyta, Acidobacteria, Bacteroidetes, Actinobacteria and Cyanobacteria were most abundant across samples. When comparing healthy and diseased L. baikalensis samples, large variations in microbial composition were found at the phylum level. Comparative analyses, which were performed for the first time for B. intermedia, showed a decrease in Chlorophyta (unicellular green algae) and an increase in Bacteroidetes and Cyanobacteria in diseased specimens. At the genus level, the Opitutus (Verrucomicrobia), Planctomyces, and Nitrospira content increased in all diseased sponges, which reflected a general tendency toward an increase in Cyanobacteria in diseased sponges. Comparative analysis of the diseased and healthy sponge metagenomes showed that diseased sponges underwent various nonspecific changes in bacterial composition. The bacterial community composition is probably influenced by sponge type and degree of disease affection.

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Assessment of Bacterial Community Composition and Dynamics in Alfalfa Silages With and Without Lactobacillus plantarum Inoculation Using Absolute Quantification 16S rRNA Sequencing

Frontiers in Microbiology ◽

10.3389/fmicb.2020.629894 ◽

2021 ◽

Vol 11 ◽

Author(s):

Fengyuan Yang ◽

Shanshan Zhao ◽

Yuan Wang ◽

Xiaomiao Fan ◽

Yanping Wang ◽

...

Keyword(s):

Bacterial Community ◽

Lactobacillus Plantarum ◽

Bacterial Abundance ◽

Bacterial Community Composition ◽

Absolute Quantification ◽

Bacterial Composition ◽

Bacterial Dna ◽

Rrna Sequencing ◽

Spearman’S Correlation ◽

Dna Amounts

Relative quantification 16S-seq (RQS) has drawn deeper insights into bacterial community compositions in silage. However, it provides no information on dynamics of the total amount of bacterial DNA through the ensiling process and across different treatments. In this study, bacterial compositions in alfalfa silage with and without Lactobacillus plantarum inoculation after 10 and 60days of ensiling were investigated using absolute quantification 16S-seq (AQS), and bacterial composition and its interaction with fermentation properties of silage indicated by AQS and RQS were compared. Variation in total bacterial DNA amounts across different treatments and ensiling periods was illustrated by AQS. AQS indicated higher bacterial richness indices and closer correlations of these indices with fermentation properties than RQS via spearman’s correlation analyses, as well as more taxa with significance on bacterial abundance via lefse analyses. In conclusion, AQS effectively illustrated the dynamics of bacterial communities during the ensiling process.

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Novel lichen-dominated hypolithic communities in the Namib Desert

Microbial Ecology ◽

10.1007/s00248-021-01812-w ◽

2021 ◽

Author(s):

Asunción de los Ríos ◽

Isaac Garrido-Benavent ◽

Alicia Limón ◽

Errol D. Cason ◽

Gillian Maggs-Kölling ◽

...

Keyword(s):

Biological Soil Crust ◽

Bacterial Community Composition ◽

Ventral Surface ◽

Namib Desert ◽

Bacterial Composition ◽

Lichen Cover ◽

Main Driver ◽

Fungal Dna ◽

Main Components ◽

First Time

AbstractThe ventral surfaces of translucent rocks from hot desert pavements often harbor hypolithic microbial communities, which are mostly dominated by cyanobacteria. The Namib Desert fog belt supports extensive hypolithic colonization of quartz rocks, which are also colonized by lichens on their dorsal surfaces. Here, we aim to evaluate whether lichens colonize the ventral surface of the rocks (i.e., show hypolithic lifestyle) and compare the bacterial composition of these coastal hypolithic communities with those found inland. Fungal DNA barcoding and fungal and bacterial Illumina metabarcoding were combined with electron microscopy to characterize the composition and spatial structure of hypolithic communities from two (coastal and inland) areas in the Namib Desert. We report, for the first time, the structure and composition of lichen-dominated hypolithic communities found in the coastal zone of the Namib Desert with extensive epilithic lichen cover. Lichen modified areoles with inverted morphology of the genus Stellarangia (three lineages) and Buellia (two lineages) were the main components of these hypolithic communities. Some of these lineages were also found in epilithic habitats. These lichen-dominated hypolithic communities differed in structural organization and bacterial community composition from those found in inland areas. The hypolithic lichen colonization characterized here seems not to be an extension of epilithic or biological soil crust lichen growths but the result of specific sublithic microenvironmental conditions. Moisture derived from fog and dew could be the main driver of this unique colonization.

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Novel Lichen-Dominated Hypolithic Communities In the Namib Desert

10.21203/rs.3.rs-382536/v1 ◽

2021 ◽

Author(s):

Asuncion de los Rios ◽

Isaac Garrido-Benavent ◽

Alicia Limón ◽

Errol D Cason ◽

Gilliam Maggs-Killing ◽

...

Keyword(s):

Biological Soil Crust ◽

Bacterial Community Composition ◽

Ventral Surface ◽

Namib Desert ◽

Bacterial Composition ◽

Lichen Cover ◽

Main Driver ◽

Fungal Dna ◽

Main Components ◽

First Time

Abstract The ventral surfaces of translucent pebbles from hot desert pavements often harbor hypolithic microbial communities, which are mostly dominated by cyanobacteria. The Namib Desert fog belt supports extensive hypolithic colonization of quartz pebbles but they are also colonized by lichens on their dorsal surfaces. Hence, our aim is to evaluate whether lichens colonize the ventral surface of the rocks (i.e., show hypolithic lifestyle) and compare the bacterial composition of these coastal hypolithic communities with those found inland. Fungal DNA barcoding and fungal and bacterial Illumina metabarcoding were combined with electron microscopy to characterize the composition and spatial structure of hypolithic communities from two (coastal and inland) areas in the Namib Desert. We report, for the first time, the structure and composition of lichen-dominated hypolithic communities found in the coastal zone of the Namib Desert with extensive epilithic lichen cover. Lichen modified areoles with inverted morphology of the genus Stellarangia (three lineages) and Buellia (two lineages) were the main components of these hypolithic communities. Some of these lineages were also found in epilithic habitats. These lichen-dominated hypolithic communities differed in structural organization and bacterial community composition from those found in inland areas. The hypolithic lichen colonization characterized here seems not to be an extension of epilithic or biological soil crust lichen growths, but the result of specific sublithic microenvironmental conditions. Moisture derived from fog and dew could be the main driver of this unique colonization.

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The first record of Gyalideopsis helvetica (Graphidaceae, lichenized Ascomycota) for Russia from the southern part of Lake Baikal Region

Novosti sistematiki nizshikh rastenii ◽

10.31111/nsnr/2015.49.282 ◽

2015 ◽

Vol 49 ◽

pp. 282-288 ◽

Cited By ~ 2

Author(s):

I. N. Urbanavichene

Keyword(s):

Lake Baikal ◽

Baikal Region ◽

First Record ◽

Identification Key ◽

Lake Baikal Region ◽

First Time

Until recently only two species of Gyalideopsis (G. piceicola and G. alnicola) were known from very few localities in Russia. Gyalideopsis helvetica is reported for the first time for Russia from the southern part of Baikal area (KhamarDaban Range, Baikalsky Zapovednik). Description of the collected specimen and its comparison with the literature data are provided; morphology, ecology and distribution of G. helvetica are discussed. The hyphophores of G. helvetica are recorded and described for the first time. An identification key to Gyalideopsis species known in Russia is provided.

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Monitoring the variation in the gut microbiota of captive woolly monkeys related to changes in diet during a reintroduction process

Scientific Reports ◽

10.1038/s41598-021-85990-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Camilo Quiroga-González ◽

Luis Alberto Chica Cardenas ◽

Mónica Ramírez ◽

Alejandro Reyes ◽

Camila González ◽

...

Keyword(s):

Gut Microbiota ◽

Site Conditions ◽

Microbiota Composition ◽

Microbial Composition ◽

Bacterial Composition ◽

Diet Diversity ◽

Woolly Monkeys ◽

The Moment ◽

Positive Effect ◽

Lagothrix Lagothricha

AbstractMicrobiome is known to play an important role in the health of organisms and different factors such as diet have been associated with modifications in microbial communities. Differences in the microbiota composition of wild and captive animals has been evaluated; however, variation during a reintroduction process in primates has never been reported. Our aim was to identify changes in the bacterial composition of three individuals of reintroduced woolly monkeys (Lagothrix lagothricha) and the variables associated with such changes. Fecal samples were collected and the V4 region of the 16S rRNA gene was sequenced to determine gut microbial composition and functionality. Individual samples from released individuals showed a higher microbial diversity after being released compared to before liberation, associated with changes in their diet. Beta diversity and functionality analysis showed separation of samples from released and captive conditions and the major factor of variation was the moment of liberation. This study shows that intestinal microbiota varies depending on site conditions and is mainly associated with diet diversity. The intake of food from wild origin by released primates may promote a positive effect on gut microbiota, improving health, and potentially increasing success in reintroduction processes.

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Xylitol enhances synthesis of propionate in the colon via cross-feeding of gut microbiota

Microbiome ◽

10.1186/s40168-021-01029-6 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Shasha Xiang ◽

Kun Ye ◽

Mian Li ◽

Jian Ying ◽

Huanhuan Wang ◽

...

Keyword(s):

Gut Microbiome ◽

Lactobacillus Reuteri ◽

Carbon Sources ◽

Short Chain Fatty Acids ◽

Microbial Composition ◽

Key Enzymes ◽

Rrna Sequencing ◽

Phosphate Acetyltransferase

Abstract Background Xylitol, a white or transparent polyol or sugar alcohol, is digestible by colonic microorganisms and promotes the proliferation of beneficial bacteria and the production of short-chain fatty acids (SCFAs), but the mechanism underlying these effects remains unknown. We studied mice fed with 0%, 2% (2.17 g/kg/day), or 5% (5.42 g/kg/day) (weight/weight) xylitol in their chow for 3 months. In addition to the in vivo digestion experiments in mice, 3% (weight/volume) (0.27 g/kg/day for a human being) xylitol was added to a colon simulation system (CDMN) for 7 days. We performed 16S rRNA sequencing, beneficial metabolism biomarker quantification, metabolome, and metatranscriptome analyses to investigate the prebiotic mechanism of xylitol. The representative bacteria related to xylitol digestion were selected for single cultivation and co-culture of two and three bacteria to explore the microbial digestion and utilization of xylitol in media with glucose, xylitol, mixed carbon sources, or no-carbon sources. Besides, the mechanisms underlying the shift in the microbial composition and SCFAs were explored in molecular contexts. Results In both in vivo and in vitro experiments, we found that xylitol did not significantly influence the structure of the gut microbiome. However, it increased all SCFAs, especially propionate in the lumen and butyrate in the mucosa, with a shift in its corresponding bacteria in vitro. Cross-feeding, a relationship in which one organism consumes metabolites excreted by the other, was observed among Lactobacillus reuteri, Bacteroides fragilis, and Escherichia coli in the utilization of xylitol. At the molecular level, we revealed that xylitol dehydrogenase (EC 1.1.1.14), xylulokinase (EC 2.7.1.17), and xylulose phosphate isomerase (EC 5.1.3.1) were key enzymes in xylitol metabolism and were present in Bacteroides and Lachnospiraceae. Therefore, they are considered keystone bacteria in xylitol digestion. Also, xylitol affected the metabolic pathway of propionate, significantly promoting the transcription of phosphate acetyltransferase (EC 2.3.1.8) in Bifidobacterium and increasing the production of propionate. Conclusions Our results revealed that those key enzymes for xylitol digestion from different bacteria can together support the growth of micro-ecology, but they also enhanced the concentration of propionate, which lowered pH to restrict relative amounts of Escherichia and Staphylococcus. Based on the cross-feeding and competition among those bacteria, xylitol can dynamically balance proportions of the gut microbiome to promote enzymes related to xylitol metabolism and SCFAs.

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Spatial scales of temperature and salinity variability estimated from Argo observations

Ocean Science Discussions ◽

10.5194/osd-12-1793-2015 ◽

2015 ◽

Vol 12 (4) ◽

pp. 1793-1814

Author(s):

F. Ninove ◽

P. Y. Le Traon ◽

E. Remy ◽

S. Guinehut

Keyword(s):

Large Scale ◽

Spatial Scales ◽

Deep Ocean ◽

General Tendency ◽

Zero Crossing ◽

Tropical Regions ◽

Covariance Functions ◽

Salinity Variability ◽

First Time

Abstract. Argo observations from 2005 to 2013 are used to characterize spatial scales temperature and salinity variations from the surface down to 1500 m. Simulations are first performed to analyze the sensitivity of results to Argo sampling; they show that several years of Argo observations are required to estimate the spatial scales of ocean variability over 20° × 20° boxes. Spatial scales are then computed over several large scale areas. Zonal and meridional spatial scales (Lx and Ly which are also zero crossing of covariance functions) vary as expected with latitudes. Scales are of about 100 km at high latitudes and more of 700 km in the Indian and Pacific equatorial/tropical regions. Zonal and meridional scales are similar: except in these tropical/equatorial regions where zonal scales are much larger (by a factor of 2 to 3) than meridional scales. Spatial scales are the largest close to the surface and have a general tendency for temperature to increase in deeper layers. There are significant differences between temperature and salinity scales, in particular, in the deep ocean. Results are consistent with previous studies based on sparse in-situ observations or satellite altimetry. They provide, however, for the first time a global description of temperature and salinity scales of variability and a characterization of their variations according to depths.

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Amazing Discoveries of Benthic Fauna from the Abyssal Zone of Lake Baikal

Biology ◽

10.3390/biology10100972 ◽

2021 ◽

Vol 10 (10) ◽

pp. 972

Author(s):

Ilya Kondratov ◽

Tatiana Sitnikova ◽

Irina Kaygorodova ◽

Natalia Denikina ◽

Vadim Annenkov ◽

...

Keyword(s):

Lake Baikal ◽

Molecular Genetic ◽

Benthic Fauna ◽

Molecular Genetic Analysis ◽

Artificial Substrates ◽

Plastic Substrate ◽

Freshwater Ecosystem ◽

Abyssal Zone ◽

First Time ◽

Natural Laboratory

Lake Baikal is a natural laboratory for the study of species diversity and evolution, as a unique freshwater ecosystem meeting the all of the main criteria of the World Heritage Convention. However, despite many years of research, the true biodiversity of the lake is clearly insufficiently studied, especially that of deep-water benthic sessile organisms. For the first time, plastic waste was raised from depths of 110 to 190 m of Lake Baikal. The aim of this study was to examine the biological community inhabiting the plastic substrate using morphological and molecular genetic analysis. Fragments of plastic packaging materials were densely populated: bryozoans, leeches and their cocoons, capsules of gastropod eggs, and turbellaria cocoons were found. All the data obtained as a result of an analysis of the nucleotide sequences of the standard bar-coding fragment of the mitochondrial genome turned out to be unique. Our results demonstrate the prospects for conducting comprehensive studies of artificial substrates to determine the true biodiversity of benthos in the abyssal zone of Lake Baikal.

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ASSESSMENT OF THE CURRENT STATE OF COASTAL WATERS OF THE SOUTHERN PART OF LAKE BAIKAL ON SANITARY AND MICROBIOLOGICAL INDICATORS WITH USE OF THE TEST SYSTEMS

ЗДОРОВЬЕ НАСЕЛЕНИЯ И СРЕДА ОБИТАНИЯ - ЗНиСО / PUBLIC HEALTH AND LIFE ENVIRONMENT ◽

10.35627/2219-5238/2018-306-9-54-58 ◽

2018 ◽

pp. 54-58

Author(s):

I.V. Mosharova ◽

V.V. Il’inskij ◽

O.V. Il’ina

Keyword(s):

Lake Baikal ◽

Coastal Waters ◽

Test Systems ◽

Current State ◽

Wide Range ◽

Microbial Number ◽

Southern Site ◽

First Time ◽

Number Of Bacteria ◽

Microbiological Indicators

Sanitary and microbiological researches of a coastal surface water of the southern part of Lake Baikal (from the Listvyanka to the Tanghui) were conducted in June, 2017. Total number of bacteria varied over a wide range – from 0.93 million сells/ml up to 2:05 million сells/ml, with an average 1.41 ± 0.3 million сells/ml. Biomass of bacteria varied from 11.05 to 305.00 mg С/m3, with an average of 123.34 mg С/m3. Coastal waters of the southern site of Lake Baikal mainly had a beta-meso-saprobic status in June, 2017. The total microbial number was determined with the use of the test systems for the first time. The values of the total microbial number were less than 1 000 COU/ml and varied from 9 to 412 COU/ml. Innovative test systems Petrifilm are of great interest for rapid assessments of the sanitary and microbiological status of reservoirs directly in the field conditions.

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Lidar profiling of aerosol optical properties from Paris to Lake Baikal (Siberia)

Atmospheric Chemistry and Physics ◽

10.5194/acp-15-5007-2015 ◽

2015 ◽

Vol 15 (9) ◽

pp. 5007-5026 ◽

Cited By ~ 19

Author(s):

E. Dieudonné ◽

P. Chazette ◽

F. Marnas ◽

J. Totems ◽

X. Shang

Keyword(s):

Optical Properties ◽

Lake Baikal ◽

Forest Fires ◽

Western Europe ◽

Lower Boundary ◽

Aerosol Optical Properties ◽

Imaging Spectrometer ◽

Moderate Resolution ◽

The Difference ◽

First Time

Abstract. In June 2013, a ground-based mobile lidar performed the ~10 000 km ride from Paris to Ulan-Ude, near Lake Baikal, profiling for the first time aerosol optical properties all the way from western Europe to central Siberia. The instrument was equipped with N2-Raman and depolarization channels that enabled an optical speciation of aerosols in the low and middle troposphere. The extinction-to-backscatter ratio (also called lidar ratio or LR) and particle depolarization ratio (PDR) at 355 nm have been retrieved. The LR in the lower boundary layer (300–700 m) was found to be 63 ± 17 sr on average during the campaign with a distribution slightly skewed toward higher values that peaks between 50 and 55 sr. Although the difference is small, PDR values observed in Russian cities (>2%, except after rain) are systematically higher than the ones measured in Europe (<1%), which is probably an effect of the lifting of terrigenous aerosols by traffic on roads. Biomass burning layers from grassland or/and forest fires in southern Russia exhibit LR values ranging from 65 to 107 sr and from 3 to 4% for the PDR. During the route, desert dust aerosols originating from the Caspian and Aral seas regions were characterized for the first time, with a LR (PDR) of 43 ± 14 sr (23 ± 2%) for pure dust. The lidar observations also showed that this dust event extended over 2300 km and lasted for ~6 days. Measurements from the Moderate Resolution Imaging Spectrometer (MODIS) show that our results are comparable in terms of aerosol optical thickness (between 0.05 and 0.40 at 355 nm) with the mean aerosol load encountered throughout our route.

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