Taxonomic Diversity Of Microbial Communities Research Articles

Habitat-related variability in the morphological and taxonomic diversity of microbial communities in two Hungarian epigenic karst caves.

The physical and chemical characteristics of the bedrock, along with the geological and hydrological conditions of karst caves may influence the taxonomic and functional diversity of prokaryotes. Most studies so far have focused on microbial communities of caves including only a few samples and have ignored the chemical heterogeneity of different habitat types such as sampling sites, dripping water, carbonate precipitates, cave walls, cave sediment and surface soils connected to the caves. The aim of the present study was to compare the morphology, the composition and physiology of the microbiota in caves with similar environmental parameters (temperature, host rock, elemental and mineral composition of speleothems) but located in different epigenic karst systems. Csodabogyós Cave and Baradla Cave (Hungary) were selected for the analysis of bacterial and archaeal communities using electron microscopy, amplicon sequencing, X-ray diffraction, and mass spectroscopic techniques. The microbial communities belonged to the phyla Pseudomonadota, Acidobacteriota, Nitrospirota and Nitrososphaerota, and they showed site-specific variation in composition and diversity. The results indicate that morphological and physiological adaptations provide survival for microorganisms according to the environment. In epigenic karst caves, prokaryotes are prone to increase their adsorption surface, cooperate in biofilms, and implement chemolithoautotrophic growth with different electron-donors and acceptors available in the microhabitats.

Taxonomic diversity of microbial communities in sub-seafloor hydrothermal sediments of the active Santorini-Kolumbo volcanic field.

Active hydrothermal vents of volcanic origin provide a remarkable manifestation of life on Earth under extreme conditions, which may have consequences for our understanding of habitability on other terrestrial bodies as well. Here, we performed for the first time Illumina sequencing of bacterial and archaeal communities on sub-seafloor samples collected from the Santorini-Kolumbo volcanic field. A total of 19 (3-m long) gravity corers were collected and processed for microbial community analysis. From a total of 6,46,671 produced V4 sequences for all samples, a total of 10,496 different Operational Taxonomic Units (OTUs) were identified that were assigned to 40 bacterial and 9 archaeal phyla and 14 candidate divisions. On average, the most abundant phyla in all samples were Chloroflexi (Chloroflexota) (24.62%), followed by Proteobacteria (Pseudomonadota) (11.29%), Firmicutes (Bacillota) (10.73%), Crenarchaeota (Thermoproteota) (8.55%), and Acidobacteria (Acidobacteriota) (8.07%). At the genus level, a total of 286 known genera and candidate genera were mostly dominated by members of Bacillus, Thermoflexus, Desulfatiglans, Pseudoalteromonas, and Pseudomonas. In most of the stations, the Chao1 values at the deeper layers were comparable to the surface sediment samples denoting the high diversity in the subsurface of these ecosystems. Heatmap analysis based on the 100 most abundant OTUs, grouped the sampling stations according to their geographical location, placing together the two hottest stations (up to 99°C). This result indicates that this specific area within the active Kolumbo crater create a distinct niche, where microorganisms with adaptation strategies to withstand heat stresses can thrive, such as the endospore-forming Firmicutes.

Razvoj raziskovalnih metod za karakterizacijo združb arbuskularnih mikoriznih gliv in potencialni vpliv biodiverzitete glivnih endofitov na vegetacijo

Karakterizacija in kvantifikacija funkcionalne in taksonomske raznolikosti mikrobnih združb je ključnega pomena za razumevanje vseh vidikov mikrobne ekologije in je povezana tudi širše z razumevanjem delovanja ekosistemov. Arbuskularna mikoriza predstavlja najbolj razširjeno in starodavno simbiozo na Zemlji, saj so arbuskularne mikorizne (AM) glive prisotne v koreninah več kot dveh tretjin vseh rastlinskih vrst. V dobrem desetletju od objave preglednega članka o uporabi molekulskih pristopov pri raziskavah arbuskularne mikorize v reviji Acta Agriculturae Slovenica (Maček, 2009) je razvoj metodologije, predvsem tehnologije določanja nukleotidnega zaporedja (sekvenciranja) naslednjih generacij (NGS), močno pospešil raziskave raznolikosti in ekologije združb AM gliv in drugih koreninskih endofitov. V tem članku so predstavljene novosti na področju raziskav endofitskih gliv v koreninah rastlin, s poudarkom na aktualnem pristopu k raziskavam v ekologiji in taksonomiji AM gliv, ter sistem njihove klasifikacije s tako imenovanimi virtualnimi taksoni (VT). Slednji je zelo uporaben za namen ekoloških raziskav in širše primerjave različnih študij med sabo. Na kratko je predstavljen tudi vpliv klimatskih in talnih lastnosti okolja na sestavo združb in pojavljanje posameznih taksonov AM gliv v različnih ekosistemih.

Prokaryotic Diversity in the Biotopes of the Gudzhirganskoe Saline Lake (Barguzin Valley, Russia)

The hydrochemical water composition and the mineralogical composition of microbial mats and bottom sediments were determined for the ephemeral saline soda lake Gudzhirganskoe (Barguzin Valley, Baikal Rift zone). Analysis of the 16S rRNA gene amplicons was applied to investigation of microbial diversity in several biotopes: brine (1 sample), sediments (3), and microbial mats (3). During sampling in October 2017, the lake was almost dry, with the residual brine (salinity 100 g/dm3) occurring occasionally, and microbial formations at two sampling points existing as dry crusts. A total of 38636 nucleotide sequences were analyzed and assigned to 193 OTUs. Bacteria predominated in all biotopes, while archaea constituted 0.013 to 4.5%. The biotopes exhibited differences in their taxonomic composition. Members of the Gammaproteobacteria (36.5%), Bacteroidetes (25.4%), and Alphaproteobacteria (18.3%) were predominant in the brine. The Gammaproteobacteria predominated (52%) in the dense dry crust (Gudzh 1-mat), while Cyanobacteria constituted only 3.4%. In the dry crust (Gudzh 2-mat), the Gammaproteobacteria also were the main component of the community (80%), primarily members of the genus Aliidiomarina (68%). In the bottom microbial mat below the residual brine, the community contained mainly Gammaproteobacteria (37.4%) and Cyanobacteria (27.8%). Firmicutes prevailed in the bottom sediments (30‒32%), while Actinobacteria (14.56%) and Deinococcus‒Thermus (15.4%) were subdominant at sampling point 1. These data made it possible to assess the present state of the lake and the taxonomic diversity of microbial communities in Lake Gudzhirganskoe biotopes.

Environmental and spatial variables determine the taxonomic but not functional structure patterns of microbial communities in alpine grasslands

There is considerable debate regarding how the taxonomic diversity of microbial communities relates to the functional diversity across space while similar questions have been explored in macro-organism communities. Here, we investigated the taxonomic and functional diversity patterns of soil microbial communities by coupling the data obtained from marker genes sequencing and functional gene surveys. Meanwhile, we evaluated the relative effects of environment and geographic distance on shaping these patterns in alpine grasslands of northern China. Although the taxonomic diversity and composition of microbial communities varied across sites, we found no consistent changes in the functional structure. Both the environmental factors and geographic distance concurrently affected the taxonomic diversity patterns but they had no effects on the spatial variations in functional genes. The functional alpha diversity was weakly correlated to the taxonomic alpha diversity across sites. Moreover, we found no significant relationship between the taxonomic and functional composition similarity among microbial communities. Together, our results provide evidence that spatial variation in microbial functions could be independent of their variations in taxonomic diversity. Even the drivers of spatial variations in the functional structure could be totally different from those of taxonomic variations such as environmental differences and dispersal limitation. Our findings suggest that spatial variations of microbial function structure within a community would not follow the variations of taxonomic structures due to different drivers between both of them over space.

Diversity of cultivated heterotrophic bacteria selected from surface waters of the Vostok Bay of the Japanese Sea

In this article, the taxonomic diversity of cultivated heterotrophic microorganisms of the surface waters of Bay Vostok of Peter the Great Bay of the Japan Sea was considered. In the bay Vostok total number of heterotrophic microorganisms was 2,0310⁵ КОЕ/ml which can be attributed to mezazoprobnye sea water. Microorganisms isolated from this coastal area are represented by 4 phylums. The cultivated microorganisms were dominated by representatives of the phylum Proteobacteria, which accounted for more than 50% of the total taxonomic diversity of the cultivated bacteria of the Vostok Bay. Phylums of Bacteroidetes, Firmicutes and Actinobacteria were also isolated. The taxonomic diversity of microbial community was represented by 15 genus. Based on the phenotypic characteristics, cultured heterotrophic bacteria was classified into the genera Rhodococcus sp., Micrococcus sp., Actynomycetes sp., Bacillus sp., Sarcina sp., Pseudomonas sp., Acinetobacter sp., Arthrobacter sp., Vibrio sp., Halomonas sp., Flavobacterium sp., Acetobacter sp., and Marinococcus sp., Pseudoalteromonas sp., Aeromonas sp., Staphylococcus sp. Sanitation-indicative bacteria in this bay were not identified, which indicates a slight anthropogenic impact. Thus bay Vostok was really insignificant recreational stress and it was reflected on marine microbial community.

Large-scale machine learning for metagenomics sequence classification

Motivation: Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is assigned to a taxonomic clade. Because of the large volume of metagenomics datasets, binning methods need fast and accurate algorithms that can operate with reasonable computing requirements. While standard alignment-based methods provide state-of-the-art performance, compositional approaches that assign a taxonomic class to a DNA read based on the k-mers it contains have the potential to provide faster solutions.Results: We propose a new rank-flexible machine learning-based compositional approach for taxonomic assignment of metagenomics reads and show that it benefits from increasing the number of fragments sampled from reference genome to tune its parameters, up to a coverage of about 10, and from increasing the k-mer size to about 12. Tuning the method involves training machine learning models on about 108 samples in 107 dimensions, which is out of reach of standard softwares but can be done efficiently with modern implementations for large-scale machine learning. The resulting method is competitive in terms of accuracy with well-established alignment and composition-based tools for problems involving a small to moderate number of candidate species and for reasonable amounts of sequencing errors. We show, however, that machine learning-based compositional approaches are still limited in their ability to deal with problems involving a greater number of species and more sensitive to sequencing errors. We finally show that the new method outperforms the state-of-the-art in its ability to classify reads from species of lineage absent from the reference database and confirm that compositional approaches achieve faster prediction times, with a gain of 2–17 times with respect to the BWA-MEM short read mapper, depending on the number of candidate species and the level of sequencing noise.Availability and implementation: Data and codes are available at http://cbio.ensmp.fr/largescalemetagenomics.Contact: pierre.mahe@biomerieux.comSupplementary information: Supplementary data are available at Bioinformatics online.

The future of skin metagenomics

Metagenomics, the direct exploitation of environmental microbial DNA, is complementary to traditional culture-based approaches for deciphering taxonomic and functional microbial diversity in a plethora of ecosystems, including those related to the human body such as the mouth, saliva, teeth, gut or skin. DNA extracted from human skin analyzed by sequencing the PCR-amplified rrs gene has already revealed the taxonomic diversity of microbial communities colonizing the human skin (“skin microbiome”). Each individual possesses his/her own skin microbial community structure, with marked taxonomic differences between different parts of the body and temporal evolution depending on physical and chemical conditions (sweat, washing etc.). However, technical limitations due to the low bacterial density at the surface of the human skin or contamination by human DNA still has inhibited extended use of the metagenomic approach for investigating the skin microbiome at a functional level. These difficulties have been overcome in part by the new generation of sequencing platforms that now provide sequences describing the genes and functions carried out by skin bacteria. These methodological advances should help us understand the mechanisms by which these microorganisms adapt to the specific chemical composition of each skin and thereby lead to a better understanding of bacteria/human host interdependence. This knowledge will pave the way for more systemic and individualized pharmaceutical and cosmetic applications.

Classification of metagenomic sequences: methods and challenges

Characterizing the taxonomic diversity of microbial communities is one of the primary objectives of metagenomic studies. Taxonomic analysis of microbial communities, a process referred to as binning, is challenging for the following reasons. Primarily, query sequences originating from the genomes of most microbes in an environmental sample lack taxonomically related sequences in existing reference databases. This absence of a taxonomic context makes binning a very challenging task. Limitations of current sequencing platforms, with respect to short read lengths and sequencing errors/artifacts, are also key factors that determine the overall binning efficiency. Furthermore, the sheer volume of metagenomic datasets also demands highly efficient algorithms that can operate within reasonable requirements of compute power. This review discusses the premise, methodologies, advantages, limitations and challenges of various methods available for binning of metagenomic datasets obtained using the shotgun sequencing approach. Various parameters as well as strategies used for evaluating binning efficiency are then reviewed.

Adapting molecular-genetic methods for studying the taxonomic diversity of microbial communities associated with macrophytes

The combination of molecular-genetic techniques used in the study is applied to investigate microorganisms associated with macrophytes. The method of enzymatic lysis with phenol-chloroform extraction is optimal for the total bacterial DNA isolation from both periphyton organisms and enriched cultures. Amplifying the total DNA on conservative primers at the two-step PCR regime is recommended. An analysis of the taxonomic diversity of the microbial community from biofilm on the reed grass and in the enriched cultures propagated on various growth media has been carried out. The results have revealed a high diversity of periphyton microorganisms associated with reed grass, including representatives of such phylogenetic lines as proteobacteria (α, β, γ, and δ subgroups), Bacteroidetes/Chlorobi, Chlamydiae/Verrucomicrobia, and cyanobacteria. The low diversity of sequences in enriched cultures is represented by dominating genotypes of Cellvibrio with a high percentage of homology and uncultivated bacilla.

Monitoring microbial community in a subsurface soil contaminated with hydrocarbons by quinone profile

A natural attenuation experiment was carried out using a lysimeter for 308 days after contaminating the subsoil with hydrocarbons (HCs) and the changes in the structures of microbial community in the hydrocarbon (HC) contaminated subsoil were monitored by quinone profile analysis. The residues of HCs remained for 217 days in the subsoil after the contamination. The amount of total quinones (TQ), an indicator of microbial biomass, significantly increased in the HC contaminated subsoil for 217 days, comparing with that of the background subsoil or the subsoil before the addition of HCs. The major quinone species and the quinone composition, indicators of community structure, were significantly different between the HC contaminated soil and the background soil for 217 days. The major increased quinine species in the HC contaminated soil were menaquinone-8(H4), menaquinone-9(H2) and ubiquinone-9, indicating the propagation of Gram-positive bacteria with high guanine and cytosine content and gamma-subclass of Proteobacteria and fungi. There was no significant difference in the diversity of the quinone species (DQ), an indicator of taxonomic diversity of microbial community, except for the decrease in DQ in the shallow subsoil after 35 days when a high concentration of HCs was detected. After 308 days when the HCs in the subsoil disappeared, TQ returned to the level of the background soil, and no significant difference in quinone composition were observed between the HC contaminated soil and the background soil. The results suggested that respiratory quinones are effective biomarkers for characterizing the temporal changes of microbial community in the HC contaminated subsoil.