scholarly journals Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6961 ◽  
Author(s):  
Guojie Cui ◽  
Jun Li ◽  
Zhaoming Gao ◽  
Yong Wang
Keyword(s):  
Microbial Communities ◽  
Sampling Site ◽  
Archaeal Community ◽  
Rrna Gene ◽  
Dominant Group ◽  
Mariana Trench ◽  
Trench Axis ◽  
Challenger Deep ◽  
The 16S Rrna Gene

Microbial communities in hadal sediments are least explored in hadal zone (>6,000 m), especially in the Challenger Deep with high pressure (∼110 M pa at the bottom). In this study, we investigated the microbial communities in the sediments of the slope and trench-axis bottom of the Challenger Deep in the Mariana Trench. Classification of the reads of the 16S rRNA gene amplicons showed vertical distribution of prokaryotic microbial inhabitants from the surface to up to 60 centimeter below surface floor (cmbsf). The most dominant phyla were Proteobacteria, Chloroflexi, Actinobacteria, Planctomycetes and candidate phyla Patescibacteria and Marinimicrobia. Distinct dominant groups in the microbial communities were observed in trench-axis sediment (water depth >8,600 m), compared to the slopes of the Challenger Deep. A sampling site at the northern slope was enriched with archaea from mesophilic Euryarchaeota Marine Group II (MGII) as a biomarker of specific geochemical setting. Among archaeal community, Thaumarchaeota represented byNitrosopumiluswere dominant in the upper layers and diminished drastically in the deeper layers. “Ca. Woesearchaeota”, however, became the dominant group in the deeper layers. Overall, our study provides a better understanding on the pattern of the microbial communities in the deepest hadal sediments on Earth, and highlights the extraordinary diversity still waiting to be discovered.

scholarly journals Collection of a Bacterial Community Reconstructed from Marine Metagenomes Derived from Jinhae Bay, South Korea

Data ◽  
2021 ◽  
Vol 6 (5) ◽  
pp. 44
Author(s):  
Jae-Hyun Lim ◽  
Il-Nam Kim
Keyword(s):  
Microbial Community ◽  
South Korea ◽  
Microbial Communities ◽  
Marine Bacteria ◽  
Sampling Site ◽  
Community Change ◽  
Rrna Gene ◽  
Water Column Stratification ◽  
Metagenomics Data ◽  
Jinhae Bay

Marine bacteria are known to play significant roles in marine biogeochemical cycles regarding the decomposition of organic matter. Despite the increasing attention paid to the study of marine bacteria, research has been too limited to fully elucidate the complex interaction between marine bacterial communities and environmental variables. Jinhae Bay, the study area in this work, is the most anthropogenically eutrophied coastal bay in South Korea, and while its physical and biogeochemical characteristics are well described, less is known about the associated changes in microbial communities. In the present study, we reconstructed a metagenomics data based on the 16S rRNA gene to investigate temporal and vertical changes in microbial communities at three depths (surface, middle, and bottom) during a seven-month period from June to December 2016 at one sampling site (J1) in Jinhae Bay. Of all the bacterial data, Proteobacteria, Bacteroidetes, and Cyanobacteria were predominant from June to November, whereas Firmicutes were predominant in December, especially at the middle and bottom depths. These results show that the composition of the microbial community is strongly associated with temporal changes. Furthermore, the community compositions were markedly different between the surface, middle, and bottom depths in summer, when water column stratification and bottom water hypoxia (low dissolved oxygen level) were strongly developed. Metagenomics data contribute to improving our understanding of important relationships between environmental characteristics and microbial community change in eutrophication-induced and deoxygenated coastal areas.

scholarly journals Psychroserpens Luteus Sp. Nov., Isolated fFrom Red Algae

2021 ◽  
Author(s):  
Xiu-Ya Ping ◽  
Kai Wang ◽  
Jin-Yu Zhang ◽  
Shu-Xin Wang ◽  
Zong-Jun Du ◽  
...  
Keyword(s):  
Red Algae ◽  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
Optimum Ph ◽  
The 16S Rrna Gene

Abstract A Gram-stain-negative, gliding-motile, positive for catalase, facultative anaerobic, designated strain XSD401T, was isolated from the red algae of Xiaoshi Island, Shandong Province, China. Growth occurred at 20–37 °C (optimum, 33 °C), pH 5.5–9.5 (optimum, pH 6.5–7.5), and with 0.5–5% (w/v) NaCl (optimum, 3%). The main fatty acids are iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, iso-C15:0 3-OH, C16:0. Phosphatidylethanolamine (PE), three unidentified aminolipids (AL1, AL2, AL3) and one unidentified lipid (L) were the major polar lipids. The G+C content of the genomic DNA was 33.9 mol%. Strain XSD401T had the highest sequence similarity (96.88%) to the 16S rRNA gene of Psychroserpens damuponensis KCTC 23539T. The similarities with Psychroserpens burtonensis DSM 12212T was 96.31%. The dDDH values between strain XSD401T and P. damuponensis KCTC 23539T, P. burtonensis DSM 12212T, were 20.40% and 20.30%, respectively. The average nucleotide identity (ANI) values between strain XSD401T and P. damuponensis KCTC 23539T, P. burtonensis DSM 12212T were 76.91%, 76.88%, respectively. The differences in morphology, physiology and genotype from the previously described taxa support the classification of strain XSD401T as a representative of a novel species of the genus Psychroserpens, for which the name Psychroserpens luteus sp. nov. is proposed. The type strain is XSD401T (= MCCC 1H00396T = KCTC 72684T = JCM 33931T).

scholarly journals Pseudomonas endophytica sp. nov., isolated from stem tissue of Solanum tuberosum L. in Spain

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2110-2117 ◽  
Author(s):  
Martha-Helena Ramírez-Bahena ◽  
Maria José Cuesta ◽  
Carmen Tejedor ◽  
José Mariano Igual ◽  
Mercedes Fernández-Pascual ◽  
...  
Keyword(s):  
Solanum Tuberosum L ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Closely Related Species ◽  
Pseudomonas Fragi ◽  
Phylogenetic Affiliation ◽  
Type Strains ◽  
The 16S Rrna Gene

A bacterial strain named BSTT44T was isolated in the course of a study of endophytic bacteria occurring in stems and roots of potato growing in a soil from Salamanca, Spain. The 16S rRNA gene sequence had 99.7 % identity with respect to that of its closest relative, Pseudomonas psychrophila E-3T, and the next most closely related type strains were those of Pseudomonas fragi, with 99.6 % similarity, Pseudomonas deceptionensis, with 99.2 % similarity, and Pseudomonas lundensis, with 99.0 % similarity; these results indicate that BSTT44T should be classified within the genus Pseudomonas. Analysis of the housekeeping genes rpoB, rpoD and gyrB confirmed its phylogenetic affiliation and showed identities lower than 92 % in all cases with respect to the above-mentioned closest relatives. Cells of the strain bore one polar–subpolar flagellum. The respiratory quinone was Q-9.The major fatty acids were C16:0, C18:1ω7c and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The strain was oxidase-, catalase- and urease-positive and the arginine dihydrolase system was present, but tests for nitrate reduction, β-galactosidase production and aesculin hydrolysis were negative. It could grow at 35 °C and at pH 5–9.The DNA G+C content was 60.2 mol%. DNA–DNA hybridization results showed less than 48 % relatedness with respect to the type strains of the four most closely related species. Therefore, the combined results of genotypic, phenotypic and chemotaxonomic analyses support the classification of strain BSTT44 into a novel species of the genus Pseudomonas, for which the name Pseudomonas endophytica sp. nov. is proposed. The type strain is BSTT44T ( = LMG 28456T = CECT 8691T).

scholarly journals STRUCTURE OF MICROBIAL COMMUNITIES OF THE ARTIFICIAL SALT CONSTRUCTIONS OF THE PERM REGION

2020 ◽  
pp. 120-127
Author(s):  
M. V. Kuznetsova ◽  
◽  
М. G. Маммаеvа ◽  
L. V. Кirichenko ◽  
M. A. Shishkin ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Staphylococcus Epidermidis ◽  
Gas Chromatography Mass Spectrometry ◽  
Rrna Gene ◽  
Genus Clostridium ◽  
Significant Difference ◽  
Viable Bacteria ◽  
Perm Region ◽  
The 16S Rrna Gene ◽  
Number Of Bacteria

The diversity of microbial communities the artificial salt constructions (ASC) located in the medicalpreventive and sanatorium institutions of the Perm region was studied. It was found that the surfaces of the abiotic salt of all ASC were contaminated with microorganisms, and a significant difference was found between the constructions of sylvinite (86.5% of positive samples) and halite (47.4%). The number of viable bacteria, as well as staphylococci, were also higher in sylvinite constructions than in halite ones. Based on bacteriological research and analysis of the 16S rRNA gene nucleotide sequences, the isolated staphylococcus strains belong to the following species: Staphylococcus epidermidis – 42.3% (n=11), S. aureus and S. saprophyticus – 19.2% (n=5), S. simulans – 7.7% (n=2) and one strain of S. cohnii urealyticum, S. hominis, S. warneri – 3.8%. The species composition of microbiocenoses formed on surfaces determined by gas chromatography–mass spectrometry included representatives of 18 genera belonging to the three main phylums: Actinobacteria, Firmicutes and Proteobacteria. Actinobacteria (Actinomyces, Corynebacterium, Nocardia, Propionibacterium, Rhodococcus, etc.) were dominant in both groups ASC. Among Firmicutes, representatives of the genus Clostridium predominated in sylvinite ASC – 63.8% of the total number of bacteria, while in halite they were half as many – 32.1%. The content of coccal microbiota, in contrast, in halite constructions was almost 3 times higher than in sylvinite. Identified quantitative and qualitative indicators of the microbiota of the ASC complement the understanding of the constructions of microbial communities under conditions of high salt load and anthropogenic impact.

scholarly journals Distinct microbial composition and functions in an underground high-temperature hot spring at different depths

2019 ◽  
Author(s):  
Shijie Bai ◽  
Xiaotong Peng
Keyword(s):  
High Temperature ◽  
Microbial Communities ◽  
Hot Springs ◽  
Hot Spring ◽  
Hydrogen Oxidation ◽  
Archaeal Community ◽  
Limited Area ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Different Depths

Abstract. The microbial diversity and functions of three high-temperature neutral hot springs water samples at different depths (0 m, 19 m and 58 m) were investigated based on 16S rRNA gene sequencing and a functional gene array (GeoChip 5.0). The results revealed that the bacterial communities were distinct at different depths in the hot springs. Additionally, in response to the depths, bacterial/archaeal community compositions exhibited shifts over the depth profiles. Aquificae, Alpha-proteobacteria, and Deinococcus-Thermus were the dominating phyla at 0 m, 19 m, and 58 m, respectively. Hydrogenobacter, Sphingobium, and Thermus were the most abundant genera at 0 m, 19 m, and 58 m, respectively. The phylum Thaumarchaeota was the most abundant member of the archaeal community in the samples at different hot spring depths. Functional results of the microbial communities indicated that microbial metabolic functions were mainly related to sulfur, nitrogen cycling, and hydrogen oxidation. In summary, our results demonstrated that distinct microbial communities and functions were found at different depths of hot springs in a very limited area. These findings will provide new insights into the deep-subsurface biosphere associated with terrestrial hot springs.

scholarly journals Dynamics and Heterogeneity of Microbial Communities in Urban Water Environments

2020 ◽  
Author(s):  
Yanqing Lian ◽  
Lisha Zhen ◽  
Xi Chen ◽  
Yang Li ◽  
Xiaona Li
Keyword(s):  
Microbial Communities ◽  
Urban Areas ◽  
Pathogenic Bacteria ◽  
Temporal Dynamics ◽  
Statistical Analyses ◽  
Polluted Water ◽  
Outer Side ◽  
Rrna Gene ◽  
The City ◽  
The 16S Rrna Gene

Abstract Water samples for the 16S rRNA gene and water quality analyses were collected from around 155 kilometers of river segments surrounding the urban areas in Xi’an of China. Multiple statistical analyses showed the temporal dynamics of microbial communities and heterogeneity in their spatial distributions. The dynamic shifts of microbial communities in the Chan, Ba, and Feng Rivers from the Spring to the Summer seasons were apparent, but little in the Zao River. The heterogeneity of microbial distributions was more due to the influence of hydrologic conditions and various sources of inflows in the rivers. The LEfSe analysis showed the Chan and Zao Rivers, both were more impacted by the sewage effluents, were more differentially abundant with bacteria related to polluted water, but the Ba and Feng Rivers, both on the outer side of the city, were more abundant with microbial communities in soil and freshwater environments in August. Multiple statistical analyses indicated that environmental variables had a significant impact on microbial communities. The GIS-based spatial analysis not only showed heterogeneity of microbial community distributions along the rivers, more importantly, could help identify locations where pathogenic bacteria presented.

Classification of ‘Anaerocellum thermophilum’ strain DSM 6725 as Caldicellulosiruptor bescii sp. nov.

2010 ◽  
Vol 60 (9) ◽  
pp. 2011-2015 ◽  
Author(s):  
Sung-Jae Yang ◽  
Irina Kataeva ◽  
Juergen Wiegel ◽  
Yanbin Yin ◽  
Phuongan Dam ◽  
...  
Keyword(s):  
New Genus ◽  
Plant Biomass ◽  
Hot Spring ◽  
Crystalline Cellulose ◽  
Rrna Gene ◽  
Growth Physiology ◽  
Caldicellulosiruptor Bescii ◽  
Untreated Plant ◽  
The 16S Rrna Gene

The thermophilic, cellulolytic, anaerobic bacterium ‘Anaerocellum thermophilum’ strain Z-1320 was isolated from a hot spring almost two decades ago and deposited in the German Collection of Microorganisms and Cell Cultures (DSMZ) as DSM 6725. The organism was classified as representing a new genus, ‘Anaerocellum’, primarily on its growth physiology, cell-wall type and morphology. The results of recent physiological studies and of phylogenetic and genome sequence analyses of strain DSM 6725 of ‘A. thermophilum’ obtained from the DSMZ showed that its properties differed from those originally described for strain Z-1320. In particular, when compared with strain Z-1320, strain DSM 6725 grew at higher temperatures and had an expanded range of growth substrates. Moreover, the 16S rRNA gene sequence of strain DSM 6725 fell within the Caldicellulosiruptor clade. It is therefore suggested that ‘Anaerocellum thermophilum’ should be classified as a member of the genus Caldicellulosiruptor, for which the name Caldicellulosiruptor bescii sp. nov. is proposed (type strain DSM 6725T=ATCC BAA-1888T). C. bescii sp. nov. DSM 6725T is the most thermophilic cellulose-degrading organism known. The strain was able to grow up to 90 °C (pH 7.2) and degraded crystalline cellulose and xylan as well as untreated plant biomass, including potential bioenergy plants such as poplar and switchgrass.

scholarly journals Usefulness of the hsp60 gene for the identification and classification of Gram-negative anaerobic rods

2010 ◽  
Vol 59 (11) ◽  
pp. 1293-1302 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Moriya Ohkuma
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gram Negative ◽  
The 16S Rrna Gene

The hsp60 gene sequences were determined for 121 strains of Gram-negative anaerobic rods, including the genera Bacteroides, Barnesiella, Butyricimonas, Odoribacter, Parabacteroides, Paraprevotella, Porphyromonas, Prevotella and Tannerella. The mean pairwise hsp60 gene sequence similarity (73.8–97.1 %) between species in each genus, except for the genus Tannerella that comprises one species, was significantly less than that of the 16S rRNA gene sequence (88.3–96.3 %). Only pairwise hsp60 gene sequence similarity (97.1 %) of the genus Paraprevotella was higher than that of the 16S rRNA gene sequence (93.8 %). Each genus formed a distinct clade in the phylogenetic analysis of the hsp60 gene sequence as well as the 16S rRNA gene sequence. The phylogenetic analysis indicated a higher evolutionary rate for the hsp60 gene sequence than the 16S rRNA gene sequence, especially in the genera Porphyromonas and Prevotella. This study suggests that the hsp60 gene is a useful alternative phylogenetic marker for the identification and classification of a broad range of Gram-negative anaerobic rods.

scholarly journals A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales

2011 ◽  
Vol 61 (12) ◽  
pp. 2984-2995 ◽  
Author(s):  
R. Thane Papke ◽  
Emma White ◽  
Prajwal Reddy ◽  
Griffin Weigel ◽  
Masahiro Kamekura ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Ribosomal Rna ◽  
Strain Analysis ◽  
Multilocus Sequence Analysis ◽  
Strain Identification ◽  
Rrna Gene ◽  
Molecular Method ◽  
Closely Related Species ◽  
The 16S Rrna Gene

Members of the order Halobacteriales are obligate extreme halophiles that belong to the domain Archaea. The classification of the Halobacteriales currently relies on a polyphasic approach, which integrates phenotypic, genotypic and chemotaxonomic characterization. However, the most utilized genetic marker for phylogeny, the 16S rRNA gene, has multiple drawbacks for use with the Halobacteriales: the species of many genera exhibit large intragenic differences between multiple ribosomal RNA operons, the gene is too conserved to discriminate reliably at the species level and it appears to be the most frequently recombined gene between closely related species. Moreover, the Halobacteriales is a rapidly expanding group due to recent successes at cultivating novel strains from a diverse set of hypersaline environments; a fast, reliable, inexpensive, portable molecular method for discriminating species is required for their investigation. Recently, multilocus sequence analysis (MLSA) has been shown to be an effective tool for strain identification and taxonomic designation, even for those taxa that experience frequent lateral gene transfer and homologous recombination. In this study, MLSA was utilized for evolutionary and taxonomic investigation of the Halobacteriales. Efficacy of the MLSA approach was tested across a hierarchical gradient using 52 halobacterial strains, representing 33 species (including names without standing in nomenclature) and 14 genera. A subset of 21 strains from the genus Haloarcula was analysed separately to test the sensitivity and relevance of the MLSA approach among closely related strains and species. The results demonstrated that MLSA differentiated individual strains, reliably grouped strains into species and species into genera and identified potential novel species and also family-like relationships. This study demonstrates that MLSA is a rapid and informative molecular method that will probably accommodate strain analysis at any taxonomic level within the Halobacteriales.

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