scholarly journals Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea

2016 ◽  
Vol 82 (5) ◽  
pp. 1599-1612 ◽  
Author(s):  
Maliheh Mehrshad ◽  
Mohammad Ali Amoozegar ◽  
Rohit Ghai ◽  
Seyed Abolhassan Shahzadeh Fazeli ◽  
Francisco Rodriguez-Valera
Keyword(s):  
Caspian Sea ◽  
Metagenomic Data ◽  
Data Sets ◽  
The Caspian Sea ◽  
Environmental Distribution ◽  
Content Type ◽  
Southern Basin ◽  
Brackish Waters ◽  
Phylogenetic Placement ◽  
Degree Of Overlap

ABSTRACTWe present here the findings from a study of the microbiome of the southern basin of the Caspian Sea, the largest water body on Earth disconnected from any ocean and a brackish inland sea. By high-throughput metagenomics, we were able to reconstruct the genomes of representative microbes. The gross community structure (at the phylum level) was different from the structure of typical marine and freshwater communities in temperate open oceans, with the Caspian Sea having freshwater-like amounts ofActinobacteriaandAlphaproteobacteria, whileGammaproteobacteriaandBetaproteobacteriawere present at intermediate levels. We assembled the genomes of several groups and provide detailed descriptions of partial genomes fromActinobacteria,Thaumarchaea, andAlphaproteobacteria. Most belonged to hitherto unknown groups, although they were related to either marine or freshwater groups. The phylogenetic placement of the Caspian genomes indicates that the organisms have multiple and separate phylogenetic origins and that they are related to organisms with both freshwater and marine lineages. Comparative recruitment from global aquatic metagenomes indicated that most Caspian microbes are endemic. However, some Caspian genomes were recruited significantly from either marine water (a member of theAlphaproteobacteria) or freshwater (a member of theActinobacteria). Reciprocally, some genomes of other origins, such as the marine thaumarchaeon “CandidatusNitrosopelagicus” or the actinobacterium “CandidatusActinomarina,” were recruited from the Caspian Sea, indicating some degree of overlap with the microbiota of other water bodies. Some of these microbes seem to have a remarkably widespread geographic and environmental distribution.

Iranian dissent will slow promised Caspian Sea accord

2018 ◽  
Keyword(s):  
Caspian Sea ◽  
Working Group ◽  
Belt And Road Initiative ◽  
Transport Networks ◽  
The Caspian Sea ◽  
Content Type ◽  
Oil Reserves ◽  
Belt And Road ◽  
Legal Position ◽  
Hydrocarbon Reserves

Subject Talks to decide the Caspian Sea's status. Significance A working group representing the five states around the Caspian Sea meets this month to prepare for a summit promised before July. The littoral states are said to be close to agreeing the legal position of the sea, but Iran's assent is far from certain. Impacts A Caspian convention will not solve contested claims to mid-sea oil reserves. Environmental protection could end up being sacrificed to the exploration and development of untapped hydrocarbon reserves. Trans-Caspian shipping will be boosted by its role in the Eurasian transport networks of China's Belt and Road initiative.

Russia wins most from Caspian deal despite concessions

2018 ◽  
Keyword(s):  
Black Sea ◽  
Coastal Waters ◽  
Caspian Sea ◽  
The Caspian Sea ◽  
Content Type

Subject Unpicking the Caspian Sea convention. Significance A convention signed by the five states around the Caspian Sea achieves a key strategic aim for Russia by excluding foreign navies and giving its warships free passage outside its neighbours' coastal waters. Iran will also be comforted by the banning of NATO and other forces. The agreement fails to rule on how subsea resources should be divided, leaving this to subsequent, possibly bilateral arrangements. Russia has conceded that Turkmenistan can lay a pipeline under the sea. Impacts Russia is offering to resume Turkmen gas purchases, reducing the urgency of a trans-Caspian pipeline. Caspian and Black Sea naval vessels will act in consort, using connecting Russian waterways. Russia has offered to prolong a moratorium on sturgeon fishing, but poaching is so common that stocks are likely to dwindle.

Scientists from Zoological Museum and Zoological Institute of RAS — researchers of biological diversity and biological resources of the Caspian Sea

2021 ◽  
pp. 56-69
Author(s):  
Aleksey Olegovich Smurov ◽  
Igor Svetozarovich\ Plotnikov ◽  
Nikolai Vasil’evic Aladin
Keyword(s):  
Caspian Sea ◽  
Biological Diversity ◽  
18Th Century ◽  
Parasite Fauna ◽  
Zoological Institute ◽  
Zoological Museum ◽  
The Caspian Sea ◽  
Brackish Waters ◽  
The Government ◽  
The 19Th Century

The origins of the study of the Caspian Sea date back to the 18th century, when the St. Petersburg Academy of Sciences was founded. The first explorers of the Caspian were academicians P.S. Pallas and S.G. Gmelin. In the 19th century, the study of Caspian fish was continued by K.E. von Baer and O.A. Grimm. Karl von Baer from 1853 to 1857 made four scientific trips to the shores of the Caspian Sea. He pioneered the fundamentals of sustainable fisheries. The main result of the expedition of K.E. von Baer — N.Ya. Danilevsky was the Charter of the Caspian fish and seal fisheries, approved by the government in 1865. According to the results of O.A. Grimm expedition 1874–1876 many new species of worms and crustaceans were discovered and it was found that from 278 species of fish, 150 are found nowhere else. The study of the biodiversity of fish and their parasite fauna in the first half of the last century was continued by scientists of the Zoological Institute N.M. Knipovich, A.N. Svetovidov, A.L. Behning, V.A. Dogel and B.E. Bykhovsky. In 2004, sciemtists of ZIN RAS published the “Catalogue of Agnathans and Fishes of Fresh and Brackish Waters of Russia with comments on nomenclature and taxonomy”, which includes valid names of taxa of agnathans and fish ranging from type to subspecies inhabiting fresh and brackish waters (up to 13 g/l) of the Azov and Caspian Seas and the freshened estuaries of the rivers of the northern and Far Eastern seas (18 orders, 43 families, 175 genera and 486 species). At present, scientists of ZIN RAS continue to study the fish resources of the Caspian Sea.

scholarly journals hypDas a Marker for [NiFe]-Hydrogenases in Microbial Communities of Surface Waters

2014 ◽  
Vol 80 (12) ◽  
pp. 3776-3782 ◽  
Author(s):  
Christian Beimgraben ◽  
Kirstin Gutekunst ◽  
Friederike Opitz ◽  
Jens Appel
Keyword(s):  
Microbial Communities ◽  
Surface Waters ◽  
Hydrogen Uptake ◽  
Metagenomic Data ◽  
Trace Gas ◽  
Sequence Motifs ◽  
Environmental Distribution ◽  
Content Type ◽  
Conserved Sequence ◽  
Conserved Sequence Motifs

ABSTRACTHydrogen is an important trace gas in the atmosphere. Soil microorganisms are known to be an important part of the biogeochemical H2cycle, contributing 80 to 90% of the annual hydrogen uptake. Different aquatic ecosystems act as either sources or sinks of hydrogen, but the contribution of their microbial communities is unknown. [NiFe]-hydrogenases are the best candidates for hydrogen turnover in these environments since they are able to cope with oxygen. As they lack sufficiently conserved sequence motifs, reliable markers for these enzymes are missing, and consequently, little is known about their environmental distribution. We analyzed the essential maturation genes of [NiFe]-hydrogenases, including their frequency of horizontal gene transfer, and foundhypDto be an applicable marker for the detection of the different known hydrogenase groups. Investigation of two freshwater lakes showed that [NiFe]-hydrogenases occur in many prokaryotic orders. We found that the respectivehypDgenes cooccur with oxygen-tolerant [NiFe]-hydrogenases (groups 1 and 5) mainly ofActinobacteria,Acidobacteria, andBurkholderiales; cyanobacterial uptake hydrogenases (group 2a) of cyanobacteria; H2-sensing hydrogenases (group 2b) ofBurkholderiales,Rhizobiales, andRhodobacterales; and two groups of multimeric soluble hydrogenases (groups 3b and 3d) ofLegionellalesand cyanobacteria. These findings support and expand a previous analysis of metagenomic data (M. Barz et al., PLoS One 5:e13846, 2010,http://dx.doi.org/10.1371/journal.pone.0013846) and further identify [NiFe]-hydrogenases that could be involved in hydrogen cycling in aquatic surface waters.

Turkmenistan cannot sell more gas despite new finds

2017 ◽  
Keyword(s):  
Economic Crisis ◽  
Foreign Investment ◽  
Caspian Sea ◽  
Oil And Gas ◽  
Energy Industry ◽  
The Caspian Sea ◽  
Content Type ◽  
Standard Response ◽  
The Government ◽  
Spending Cuts

Subject Turkmenistan's oil and gas prospects. Significance Turkmenistan has among the largest global gas reserves and recently reported a promising new find, but its limited export options and low gas revenues have led to economic crisis. The government has responded with energy industry personnel changes, spending cuts and a bid to attract more foreign investment. Impacts Shortages of goods and cash may lead to more local protests, which have so far been rare in this repressive state. The standard response of blaming sacking officials is looking less and less adequate. Turkmenistan may examine ways of getting gas across the Caspian Sea without building a full pipeline.

scholarly journals Humans Are Selectively Exposed to Pneumocystis jirovecii

mBio ◽  
2020 ◽  
Vol 11 (2) ◽  
Author(s):  
Ousmane H. Cissé ◽  
Liang Ma ◽  
Chao Jiang ◽  
Michael Snyder ◽  
Joseph A. Kovacs
Keyword(s):  
Fungal Spore ◽  
Airborne Fungi ◽  
Pneumocystis Jirovecii ◽  
Metagenomic Data ◽  
Transmission Model ◽  
Data Sets ◽  
Shotgun Metagenomics ◽  
Content Type ◽  
Environmental Reservoir ◽  
The Impact

ABSTRACT Environmental exposure has a significant impact on human health. While some airborne fungi can cause life-threatening infections, the impact of environment on fungal spore dispersal and transmission is poorly understood. The democratization of shotgun metagenomics allows us to explore important questions about fungal propagation. We focus on Pneumocystis, a genus of host-specific fungi that infect mammals via airborne particles. In humans, Pneumocystis jirovecii causes lethal infections in immunocompromised patients if untreated, although its environmental reservoir and transmission route remain unclear. Here, we attempt to clarify, by analyzing human exposome metagenomic data sets, whether humans are exposed to different Pneumocystis species present in the air but only P. jirovecii cells are able to replicate or whether they are selectively exposed to P. jirovecii. Our analysis supports the latter hypothesis, which is consistent with a local transmission model. These data also suggest that healthy carriers are a major driver for the transmission.

scholarly journals The Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal Sample

2021 ◽  
Vol 87 (6) ◽  
Author(s):  
Alexandra Meziti ◽  
Luis M. Rodriguez-R ◽  
Janet K. Hatt ◽  
Angela Peña-Gonzalez ◽  
Karen Levy ◽  
...  
Keyword(s):  
Natural Populations ◽  
Housekeeping Genes ◽  
Metagenomic Data ◽  
Data Sets ◽  
Data Set ◽  
Content Type ◽  
Population Variable ◽  
Metagenome Assembly ◽  
Variable Genes ◽  
Core Genes

ABSTRACT The recovery of metagenome-assembled genomes (MAGs) from metagenomic data has recently become a common task for microbial studies. The strengths and limitations of the underlying bioinformatics algorithms are well appreciated by now based on performance tests with mock data sets of known composition. However, these mock data sets do not capture the complexity and diversity often observed within natural populations, since their construction typically relies on only a single genome of a given organism. Further, it remains unclear if MAGs can recover population-variable genes (those shared by >10% but <90% of the members of the population) as efficiently as core genes (those shared by >90% of the members). To address these issues, we compared the gene variabilities of pathogenic Escherichia coli isolates from eight diarrheal samples, for which the isolate was the causative agent, against their corresponding MAGs recovered from the companion metagenomic data set. Our analysis revealed that MAGs with completeness estimates near 95% captured only 77% of the population core genes and 50% of the variable genes, on average. Further, about 5% of the genes of these MAGs were conservatively identified as missing in the isolate and were of different (non-Enterobacteriaceae) taxonomic origin, suggesting errors at the genome-binning step, even though contamination estimates based on commonly used pipelines were only 1.5%. Therefore, the quality of MAGs may often be worse than estimated, and we offer examples of how to recognize and improve such MAGs to sufficient quality by (for instance) employing only contigs longer than 1,000 bp for binning. IMPORTANCE Metagenome assembly and the recovery of metagenome-assembled genomes (MAGs) have recently become common tasks for microbiome studies across environmental and clinical settings. However, the extent to which MAGs can capture the genes of the population they represent remains speculative. Current approaches to evaluating MAG quality are limited to the recovery and copy number of universal housekeeping genes, which represent a small fraction of the total genome, leaving the majority of the genome essentially inaccessible. If MAG quality in reality is lower than these approaches would estimate, this could have dramatic consequences for all downstream analyses and interpretations. In this study, we evaluated this issue using an approach that employed comparisons of the gene contents of MAGs to the gene contents of isolate genomes derived from the same sample. Further, our samples originated from a diarrhea case-control study, and thus, our results are relevant for recovering the virulence factors of pathogens from metagenomic data sets.

scholarly journals Stability of the Virome in Lab- and Field-Collected Aedes albopictus Mosquitoes across Different Developmental Stages and Possible Core Viruses in the Publicly Available Virome Data of Aedes Mosquitoes

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Chenyan Shi ◽  
Lu Zhao ◽  
Evans Atoni ◽  
Weifeng Zeng ◽  
Xiaomin Hu ◽  
...  
Keyword(s):  
Aedes Albopictus ◽  
Developmental Stages ◽  
Metagenomic Data ◽  
Data Sets ◽  
Transmission Route ◽  
Content Type ◽  
The Core ◽  
Aedes Mosquitoes ◽  
Arbovirus Infection ◽  
Over Time

Our study revealed that the virome was very stable across all developmental stages of both lab-derived and field-collected Aedes albopictus. The data representing the core virome in lab A. albopictus proved the vertical transmission route of these viruses, forming a “vertically transmitted core virome.” Field mosquitoes also contained this stable vertically transmitted core virome as well as additional viruses, which probably represented “environment-derived core virome” and which therefore were less stable over time and geography. By further screening publicly available SRA viral metagenomic data sets from mosquitoes belonging to the genus Aedes, some of the identified core ISVs were shown to be present in the majority of SRAs, such as Phasi Charoen-like phasivirus and Guadeloupe mosquito virus. How these core ISVs influence the biology of the mosquito host and arbovirus infection and evolution deserves to be further explored.

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