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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Systems Microbiology".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 27496

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Prof. Dr. Olga V. Karnachuk

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Department of Plant Physiology, Biotechnology and Bioinformatics, Tomsk State University, Lenin St., 36, 634050 Tomsk, Russia
Interests: anaerobic microorganisms; deep biosphere; extremophiles; sulfidogenic prokaryotes; human and animal gut microbiote; biomineralization

Special Issue Information

Dear Colleagues,

Recent achievements in sequencing techniques and bioinformatics tools have greatly expanded the known diversity of Bacteria and Archaea, and postulated the overwhelming majority of uncultured prokaryotes in our planet’s environments. Culture-independent genomic analysis and metagenomics are essential to understand microbial diversity, metabolism, and the prospective industrial applications of microorganisms. On the other hand, metabolic reconstructions deduced from metagenome-assembled genomes (MAGs) and single-cell genomes (SAGs) provide clues for improving the cultivation of yet-uncultivated microorganisms.

The aim of this Special Issue of Microorganisms is to present a collection of articles that provide insight into genomic analysis in different biotopes, including various types of marine and terrestrial habitats. We also welcome reviews and research articles dedicated to human and animal microbiomes as well as artificial environments.

Prof. Dr. Olga V. Karnachuk
Guest Editor

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Keywords

metagenome
microbiome
genome
metagenome-assembled genomes
uncultivated microorganisms

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Published Papers (10 papers)

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16 pages, 4113 KiB

Open AccessArticle

Aqueous Geochemical Controls on the Sestonic Microbial Community in Lakes Michigan and Superior

by Asha Rani, Ravi Ranjan, Solidea M. C. Bonina, Mahsa Izadmehr, John P. Giesy, An Li, Neil C. Sturchio and Karl J. Rockne

Microorganisms 2023, 11(2), 504; https://doi.org/10.3390/microorganisms11020504 - 17 Feb 2023

Viewed by 3058

Abstract

Despite being the largest freshwater lake system in the world, relatively little is known about the sestonic microbial community structure in the Laurentian Great Lakes. The goal of this research was to better understand this ecosystem using high-throughput sequencing of microbial communities as a function of water depth at six locations in the westernmost Great Lakes of Superior and Michigan. The water column was characterized by gradients in temperature, dissolved oxygen (DO), pH, and other physicochemical parameters with depth. Mean nitrate concentrations were 32 μmol/L, with only slight variation within and between the lakes, and with depth. Mean available phosphorus was 0.07 μmol/L, resulting in relatively large N:P ratios (97:1) indicative of P limitation. Abundances of the phyla Actinobacteria, Bacteroidetes, Cyanobacteria, Thaumarchaeota, and Verrucomicrobia differed significantly among the Lakes. Candidatus Nitrosopumilus was present in greater abundance in Lake Superior compared to Lake Michigan, suggesting the importance of ammonia-oxidating archaea in water column N cycling in Lake Superior. The Shannon diversity index was negatively correlated with pH, temperature, and salinity, and positively correlated with DO, latitude, and N₂ saturation. Results of this study suggest that DO, pH, temperature, and salinity were major drivers shaping the community composition in the Great Lakes. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in the Environment)

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14 pages, 1947 KiB

Open AccessArticle

Carbon Emission and Biodiversity of Arctic Soil Microbial Communities of the Novaya Zemlya and Franz Josef Land Archipelagos

by Zorigto Namsaraev, Anna Bobrik, Aleksandra Kozlova, Anastasia Krylova, Anastasia Rudenko, Anastasia Mitina, Aleksandr Saburov, Maksim Patrushev, Olga Karnachuk and Stepan Toshchakov

Microorganisms 2023, 11(2), 482; https://doi.org/10.3390/microorganisms11020482 - 15 Feb 2023

Cited by 4 | Viewed by 2217

Abstract

Cryogenic soils are the most important terrestrial carbon reservoir on the planet. However, the relationship between soil microbial diversity and CO₂ emission by cryogenic soils is poorly studied. This is especially important in the context of rising temperatures in the high Arctic which can lead to the activation of microbial processes in soils and an increase in carbon input from cryogenic soils into the atmosphere. Here, using high-throughput sequencing of 16S rRNA gene amplicons, we analyzed microbial community composition and diversity metrics in relation to soil carbon dioxide emission, water-extractable organic carbon and microbial biomass carbon in the soils of the Barents Sea archipelagos, Novaya Zemlya and Franz Josef Land. It was found that the highest diversity and CO₂ emission were observed on the Hooker and Heiss Islands of the Franz Josef Land archipelago, while the diversity and CO₂ emission levels were lower on Novaya Zemlya. Soil moisture and temperature were the main parameters influencing the composition of soil microbial communities on both archipelagos. The data obtained show that CO₂ emission levels and community diversity on the studied islands are influenced mostly by a number of local factors, such as soil moisture, microclimatic conditions, different patterns of vegetation and fecal input from animals such as reindeer. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in the Environment)

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13 pages, 3199 KiB

Open AccessArticle

Active Sulfate-Reducing Bacterial Community in the Camel Gut

by Olga V. Karnachuk, Inna A. Panova, Vasilii L. Panov, Olga P. Ikkert, Vitaly V. Kadnikov, Igor I. Rusanov, Marat R. Avakyan, Lubov B. Glukhova, Anastasia P. Lukina, Anatolii V. Rakitin, Shahjahon Begmatov, Alexey V. Beletsky, Nikolai V. Pimenov and Nikolai V. Ravin

Microorganisms 2023, 11(2), 401; https://doi.org/10.3390/microorganisms11020401 - 4 Feb 2023

Cited by 6 | Viewed by 2088

Abstract

The diversity and activity of sulfate-reducing bacteria (SRB) in the camel gut remains largely unexplored. An abundant SRB community has been previously revealed in the feces of Bactrian camels (Camelus bactrianus). This study aims to combine the 16S rRNA gene profiling, sulfate reduction rate (SRR) measurement with a radioactive tracer, and targeted cultivation to shed light on SRB activity in the camel gut. Fresh feces of 55 domestic Bactrian camels grazing freely on semi-arid mountain pastures in the Kosh-Agach district of the Russian Altai area were analyzed. Feces were sampled in early winter at an ambient temperature of −15 °C, which prevented possible contamination. SRR values measured with a radioactive tracer in feces were relatively high and ranged from 0.018 to 0.168 nmol S cm⁻³ day⁻¹. The 16S rRNA gene profiles revealed the presence of Gram-negative Desulfovibrionaceae and spore-forming Desulfotomaculaceae. Targeted isolation allowed us to obtain four pure culture isolates belonging to Desulfovibrio and Desulforamulus. An active SRB community may affect the iron and copper availability in the camel intestine due to metal ions precipitation in the form of sparingly soluble sulfides. The copper-iron sulfide, chalcopyrite (CuFeS₂), was detected by X-ray diffraction in 36 out of 55 analyzed camel feces. In semi-arid areas, gypsum, like other evaporite sulfates, can be used as a solid-phase electron acceptor for sulfate reduction in the camel gastrointestinal tract. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in the Environment)

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14 pages, 1255 KiB

Open AccessArticle

Bacterial Communities of Lamiacea L. Medicinal Plants: Structural Features and Rhizosphere Effect

by Ekaterina K. Zharkova, Anna A. Vankova, Olga V. Selitskaya, Elena L. Malankina, Natalya V. Drenova, Alena D. Zhelezova, Vitaliy K. Khlyustov, Sergey L. Belopukhov, Aleksey V. Zhevnerov, Ludmila A. Sviridova, Tatiana N. Fomina and Andrey V. Kozlov

Microorganisms 2023, 11(1), 197; https://doi.org/10.3390/microorganisms11010197 - 12 Jan 2023

Cited by 2 | Viewed by 2565

Abstract

Bacterial communities associated with medicinal plants are an essential part of ecosystems. The rhizosphere effect is rather important in the cultivation process. The purpose of the study was to analyze the rhizosphere effect of oregano (Origanum vulgare L.), peppermint (Mentha piperita L.), thyme (Thymus vulgaris L.), creeping thyme (Thymus serpillum L.) and sage (Salvia officinalis L.). To estimate the quantity of 16S bacteria ribosomal genes, qPCR assays were used. To compare bacterial communities’ structure of medicinal plants rhizosphere with bulk soil high-throughput sequencing of the 16S rRNA targeting variable regions V3–V4 of bacteria was carried out. The highest bacterial abundance was associated with T. vulgaris L., M. piperita L. and S. officinalis L., and the lowest was associated with the O. vulgare L. rhizosphere. Phylum Actinobacteriota was predominant in all rhizosphere samples. The maximum bacterial α-diversity was found in S. officinalis L. rhizosphere. According to bacterial β-diversity calculated by the Bray–Curtis metric, T. vulgaris L. root zone significantly differed from bulk soil. The rhizosphere effect was positive to the Myxococcota, Bacteroidota, Verrucomicrobiota, Proteobacteria and Gemmatimonadota. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in the Environment)

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13 pages, 950 KiB

Open AccessArticle

Distribution Patterns of Antibiotic Resistance Genes and Their Bacterial Hosts in a Manure Lagoon of a Large-Scale Swine Finishing Facility

by Shahjahon Begmatov, Alexey V. Beletsky, Eugeny V. Gruzdev, Andrey V. Mardanov, Lubov B. Glukhova, Olga V. Karnachuk and Nikolai V. Ravin

Microorganisms 2022, 10(11), 2301; https://doi.org/10.3390/microorganisms10112301 - 20 Nov 2022

Cited by 7 | Viewed by 2590

Abstract

The spread of antibiotic resistance genes (ARGs) that are present in livestock manures, which are discharged into the environment, is a severe threat to human and animal health. Here, we used 16S rRNA gene profiling and metagenomic analysis to characterize microbial community composition and antibiotic resistance in a manure storage lagoon from a large-scale swine finishing facility. Manure samples were collected at intervals of two years. Both the prokaryotic community and the resistome were dominated by the Firmicutes, Proteobacteria and Bacteroidota. Metagenomic analysis of two samples revealed 726 and 641 ARGs classified into 59 and 46 AMR gene families. Besides multidrug efflux pumps, the predominating ARGs potentially encoded resistance to tetracyclines, macrolide–lincosamide–streptogramin, aminoglycosides, peptide antibiotics, rifamycin, chloramphenicol, and beta-lactams. Genes from all predominant AMR gene families were found in both samples indicating overall long-term stability of the resistome. Antibiotic efflux pumps were the primary type of ARGs in the Proteobacteria, while antibiotic target alteration or protection was the main mechanism of resistance in the Firmicutes, Actinobacteriota and Bacteroidota. Metagenome-assembled genomes (MAG) of four multidrug-resistant strains were assembled. The first MAG, assigned to Escherichia flexneri, contained 46 ARGs, including multidrug efflux pumps, modified porins, beta-lactamases, and genes conferring resistance to peptide antibiotics. The second MAG, assigned to the family Alcaligenaceae, contained 18 ARGs encoding resistance to macrolide–lincosamide–streptogramin, tetracyclines, aminoglycosides and diaminopyrimidins. Two other MAGs representing the genera Atopostipes and Prevotella, contained four and seven ARGs, respectively. All these MAGs represented minor community members and accounted for less than 0.3% of the whole metagenome. Overall, a few lineages originated from the gut but relatively rare in the manure storage lagoon, are the main source of ARGs and some of them carry multiple resistance determinants. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in the Environment)

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15 pages, 2419 KiB

Open AccessArticle

Microbial Community in the Permafrost Thaw Gradient in the South of the Vitim Plateau (Buryatia, Russia)

by Svetlana Zaitseva, Nimazhap Badmaev, Lyudmila Kozyreva, Vyacheslav Dambaev and Darima Barkhutova

Microorganisms 2022, 10(11), 2202; https://doi.org/10.3390/microorganisms10112202 - 7 Nov 2022

Cited by 3 | Viewed by 2099

Abstract

Soil microbial communities play key roles in biogeochemical cycles and greenhouse gas formation during the decomposition of the released organic matter in the thawing permafrost. The aim of our research was to assess the taxonomic prokaryotic diversity in soil-ecological niches of the Darkhituy-Khaimisan transect during the initial period of soil thawing. We investigated changes in the microbial communities present in the active layer of four sites representing distinct habitats (larch forest, birch forest, meadow steppe and thermokarst lake). We explore the relationship between the biogeochemical differences among habitats and the active layer microbial community via a spatial (across habitats, and with depth through the active layer) community survey using high-throughput Illumina sequencing. Microbial communities showed significant differences between active and frozen layers and across ecosystem types, including a high relative abundance of Alphaproteobacteria, Firmicutes, Crenarchaeota, Bacteroidota and Gemmatimonadota in the active layer and a high relative abundance of Actinobacteriota and Desulfobacterota in the frozen layer. Soil pH, temperature and moisture were the most significant parameters underlying the variations in the microbial community composition. CCA suggested that the differing environmental conditions between the four soil habitats had strong influences on microbial distribution and diversity and further explained the variability of soil microbial community structures. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in the Environment)

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19 pages, 2492 KiB

Open AccessArticle

Microbial Communities of Artisanal Fermented Milk Products from Russia

by Tatiana V. Kochetkova, Ilya P. Grabarnik, Alexandra A. Klyukina, Kseniya S. Zayulina, Ivan M. Elizarov, Oksana O. Shestakova, Liliya A. Gavirova, Anastasia D. Malysheva, Polina A. Shcherbakova, Darima D. Barkhutova, Olga V. Karnachuk, Andrey I. Shestakov, Alexander G. Elcheninov and Ilya V. Kublanov

Microorganisms 2022, 10(11), 2140; https://doi.org/10.3390/microorganisms10112140 - 29 Oct 2022

Cited by 12 | Viewed by 3601

Abstract

Fermented milk products (FMPs) have numerous health properties, making them an important part of our nutrient budget. Based on traditions, history and geography, there are different preferences and recipes for FMP preparation in distinct regions of the world and Russia in particular. A number of dairy products, both widely occurring and region-specific, were sampled in the households and local markets of the Caucasus republics, Buryatia, Altai, and the Far East and European regions of Russia. The examined FMPs were produced from cow, camel, mare’s or mixed milk, in the traditional way, without adding commercial starter cultures. Lactate and acetate were the major volatile fatty acids (VFA) of the studied FMPs, while succinate, formate, propionate and n-butyrate were present in lower concentrations. Bacterial communities analyzed by 16S rRNA gene V4 fragment amplicon sequencing showed that Firmicutes (Lactococcus, Lactobacillus, Streptococcus, Lentilactobacillus and Leuconostoc) was the predominant phylum in all analyzed FMPs, followed by Proteobacteria (Acetobacter, Klebsiella, Pseudomonas and Citrobacter). Lactobacillus (mainly in beverages) or Lactococcus (mainly in creamy and solid products) were the most abundant community-forming genera in FMPs where raw milk was used and fermentation took place at (or below) room temperature. In turn, representatives of Streptococcus genus dominated the FMPs made from melted or pasteurized milk and fermented at elevated temperatures (such as ryazhenka, cottage cheese and matsoni-like products). It was revealed that the microbial diversity of koumiss, shubat, ryazhenka, matsoni-like products, chegen, sour cream and bryndza varied slightly within each type and correlated well with the same products from other regions and countries. On the other hand, the microbiomes of kefir, prostokvasha, ayran, cottage cheese and suluguni-like cheese were more variable and were shaped by the influence of particular factors linked with regional differences and traditions expressed in specificities in the production process. The microbial diversity of aarts, khurunga, khuruud, tan, ayran and suluguni-like cheese was studied here, to our knowledge, for the first time. The results of this study emphasize the overall similarity of the microbial communities of various FMPs on the one hand, and specificities of regional products on the other. The latter are of particular value in the age of globalization when people have begun searching for new and unusual products and properties. Speaking more specifically, these novel products, with their characteristic communities, might be used for the development of novel microbial associations (i.e., starters) to produce novel products with improved or unique properties. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in the Environment)

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22 pages, 2682 KiB

Open AccessArticle

Microbial Communities of Seawater and Coastal Soil of Russian Arctic Region and Their Potential for Bioremediation from Hydrocarbon Pollutants

by Ekaterina M. Semenova, Tamara L. Babich, Diyana S. Sokolova, Alexey P. Ershov, Yeva I. Raievska, Salimat K. Bidzhieva, Alexey L. Stepanov, Maria V. Korneykova, Vladimir A. Myazin and Tamara N. Nazina

Microorganisms 2022, 10(8), 1490; https://doi.org/10.3390/microorganisms10081490 - 24 Jul 2022

Cited by 14 | Viewed by 3496

Abstract

The development of Arctic regions leads to pollution of marine and coastal environments with oil and petroleum products. The purpose of this work was to determine the diversity of microbial communities in seawater, as well as in littoral and coastal soil, and the potential ability of their members to degrade hydrocarbons degradation and to isolate oil-degrading bacteria. Using high-throughput sequencing of the V4 region of the 16S rRNA gene, the dominance of bacteria in polar communities was shown, the proportion of archaea did not exceed 2% (of the total number of sequences in the libraries). Archaea inhabiting the seawater belonged to the genera Nitrosopumilus and Nitrosoarchaeum and to the Nitrososphaeraceae family. In the polluted samples, members of the Gammaproteobacteria, Alphaproteobacteria, and Actinomycetes classes predominated; bacteria of the classes Bacteroidia, Clostridia, Acidimicrobiia, Planctomycetia, and Deltaproteobacteria were less represented. Using the iVikodak program and KEGG database, the potential functional characteristics of the studied prokaryotic communities were predicted. Bacteria were potentially involved in nitrogen and sulfur cycles, in degradation of benzoate, terephthalate, fatty acids, and alkanes. A total of 19 strains of bacteria of the genera Pseudomonas, Aeromonas, Oceanisphaera, Shewanella, Paeniglutamicibacter, and Rhodococcus were isolated from the studied samples. Among them were psychrotolerant and psychrophilic bacteria growing in seawater and utilizing crude oil, diesel fuel, and motor oils. The data obtained suggest that the studied microbial communities could participate in the removal of hydrocarbons from arctic seawater and coastal soils and suggested the possibility of the application of the isolates for the bioaugmentation of oil-contaminated polar environments. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in the Environment)

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13 pages, 2227 KiB

Open AccessArticle

Two New Species of Filamentous Sulfur Bacteria of the Genus Thiothrix, Thiothrix winogradskyi sp. nov. and ‘Candidatus Thiothrix sulfatifontis’ sp. nov.

by Nikolai V. Ravin, Simona Rossetti, Alexey V. Beletsky, Vitaly V. Kadnikov, Tatyana S. Rudenko, Dmitry D. Smolyakov, Marina I. Moskvitina, Maria V. Gureeva, Andrey V. Mardanov and Margarita Yu. Grabovich

Microorganisms 2022, 10(7), 1300; https://doi.org/10.3390/microorganisms10071300 - 27 Jun 2022

Cited by 9 | Viewed by 3187 | Correction

Abstract

The metagenome of foulings from sulfidic spring “Serovodorodny” (Tatarstan, Russia), where members of the genus Thiothrix was observed, was sequenced. Representatives of the phyla Gammaproteobacteria, Cyanobacteria and Campilobacteriota dominated in the microbial community. The complete genome of Thiothrix sp. KT was assembled from the metagenome. It displayed 93.93–99.72% 16S rRNA gene sequence identity to other Thiothrix species. The average nucleotide identity (ANI) и digital DNA-DNA hybridization (dDDH) showed that the genome designated KT represents a new species within the genus Thiothrix, ‘Candidatus Thiothrix sulfatifontis’ sp. nov. KT. The taxonomic status has been determined of the strain Thiothrix sp. CT3, isolated about 30 years ago and not assigned to any of Thiothrix species due to high 16S rRNA gene sequence identity with related species (i.e., 98.8–99.4%). The complete genome sequence of strain CT3 was determined. The ANI between CT3 and other Thiothrix species was below 82%, and the dDDH values were less than 40%, indicating that strain CT3 belongs to a novel species, Thiothrix winogradskyi sp. nov. A genome analysis showed that both strains are chemo-organoheterotrophs, chemolithotrophs (in the presence of hydrogen sulfide and thiosulfate) and chemoautotrophs. For the first time, representatives of Thiothrix showed anaerobic growth in the presence of thiosulfate. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in the Environment)

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3 pages, 186 KiB

Open AccessCorrection

Correction: Ravin et al. Two New Species of Filamentous Sulfur Bacteria of the Genus Thiothrix, Thiothrix winogradskyi sp. nov. and ‘Candidatus Thiothrix sulfatifontis’ sp. nov. Microorganisms 2022, 10, 1300

Microorganisms 2022, 10(8), 1665; https://doi.org/10.3390/microorganisms10081665 - 18 Aug 2022

Cited by 1 | Viewed by 1252

Abstract

The authors wish to make the following corrections to this paper [...] Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in the Environment)

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