scholarly journals Deciphering the origin and metabolic potential of deeply buried sediment bacteria in the deep biosphere

2021 ◽  
Author(s):  
Jiahua Wang ◽  
Xin Hu ◽  
Jiasong Fang
Keyword(s):  
Deep Biosphere ◽  
Metabolic Potential ◽  
Sediment Bacteria

scholarly journals Metagenomic Investigation of a Low Diversity, High Salinity Offshore Oil Reservoir

2021 ◽  
Vol 9 (11) ◽  
pp. 2266
Author(s):  
Gabrielle Scheffer ◽  
Casey R. J. Hubert ◽  
Dennis R. Enning ◽  
Sven Lahme ◽  
Jaspreet Mand ◽  
...  
Keyword(s):  
Oil Recovery ◽  
High Salinity ◽  
Extreme Environments ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Oil Reservoir ◽  
Deep Biosphere ◽  
Metabolic Potential ◽  
Microbial Life ◽  
Saline Formation

Oil reservoirs can represent extreme environments for microbial life due to low water availability, high salinity, high pressure and naturally occurring radionuclides. This study investigated the microbiome of saline formation water samples from a Gulf of Mexico oil reservoir. Metagenomic analysis and associated anaerobic enrichment cultures enabled investigations into metabolic potential for microbial activity and persistence in this environment given its high salinity (4.5%) and low nutrient availability. Preliminary 16S rRNA gene amplicon sequencing revealed very low microbial diversity. Accordingly, deep shotgun sequencing resulted in nine metagenome-assembled genomes (MAGs), including members of novel lineages QPJE01 (genus level) within the Halanaerobiaceae, and BM520 (family level) within the Bacteroidales. Genomes of the nine organisms included respiratory pathways such as nitrate reduction (in Arhodomonas, Flexistipes, Geotoga and Marinobacter MAGs) and thiosulfate reduction (in Arhodomonas, Flexistipes and Geotoga MAGs). Genomic evidence for adaptation to high salinity, withstanding radioactivity, and metal acquisition was also observed in different MAGs, possibly explaining their occurrence in this extreme habitat. Other metabolic features included the potential for quorum sensing and biofilm formation, and genes for forming endospores in some cases. Understanding the microbiomes of deep biosphere environments sheds light on the capabilities of uncultivated subsurface microorganisms and their potential roles in subsurface settings, including during oil recovery operations.

Dry and storm weather transport of coliforms and faecal streptococci in combined sewage

1995 ◽  
Vol 31 (7) ◽  
pp. 311-320 ◽  
Author(s):  
R. M. Ashley ◽  
W. Dabrowski
Keyword(s):  
Data Collection ◽  
Coliform Bacteria ◽  
Pathogenic Microorganisms ◽  
Chemical Parameters ◽  
Physical Chemical ◽  
Sediment Bacteria ◽  
Wet Weather ◽  
Faecal Streptococci

Combined sewage coliform bacteria are important as indicators of pathogenic microorganisms and of their possible discharge into the environment. Whilst specifying limits for viruses, most legislation recognises the difficulty of enumerating such organisms and also prescribes limits for coliforms. Despite the importance of these organisms, little is known about their numbers and behaviour in sewerage systems. A data collection programme is described which has monitored dry and wet weather sewage coliform bacteria and also sediment bacteria. These data are used to review recent UK recommendations for assessing bacteria numbers in storm discharges. It is concluded that relationships between bacteria numbers and other physical/chemical parameters may be developed during DWF, but are seasonally and catchment dependent. Extension of DWF measurements to predict storm bacteria may be possible with more data.

LC-MS/MS Method Development and Validation for the Determination of Ilexsaponin A1 and Its Application in Intestinal Bacterial Metabolic Study

2020 ◽  
Vol 16 (6) ◽  
pp. 774-781
Author(s):  
Liang Wu ◽  
An Kang ◽  
Yujie Lin ◽  
Chenxiao Shan ◽  
Zhu Zhou ◽  
...  
Keyword(s):  
Method Development ◽  
Ischemia Reperfusion ◽  
Scientific Evidence ◽  
Potential Effect ◽  
Bacterial Strains ◽  
Metabolic Potential ◽  
Bifidobacterium Adolescentis ◽  
Metabolic Behavior ◽  
And Behavior

Background: Ilexsaponin A1, one of the most representative triterpene saponin components in the roots of I. pubescens, showed its effects in anticoagulation and antithrombosis, attenuating ischemia-reperfusion-induced myocardial, angiogenesis and inhibiting phosphodiesterase. Objective: Reveal the key intestinal bacterial strains responsible for ilexsaponin A1 metabolism, and clarify their metabolic behavior. Methods: An accurate and sensitive LC-MS/MS method for the determination of “ilexsaponin A1 in General Anaerobic Medium (GAM) broth” was established and systematically validated. Then it was applied to screen and study the metabolic potential of the intestinal bacterial strains in an anaerobic incubation system. Results: Quantitation of ilexsaponin A1 could be performed within an analytical run time of 14.5 min, in the linear range of 2 - 2000 ng/ml. Enterobacter sakazakii, Bifidobacterium breve, Bifidobacterium adolescentis, Bifidobacterium catenulatum, and Bifidobacterium angulatum were identified to have a potential effect to metabolize ilexsaponin A1 to different extents; and further bacterial metabolic studies were performed to clarify their metabolic capacity and behavior. Conclusion: This paper contributes to a better understanding of the intestinal bacterial metabolism of ilexsaponin A1 and provides scientific evidence for its clinical application. Additionally, the importance of intestinal bacterial strains in the disposition of natural products was also highlighted.

scholarly journals The Fennoscandian Shield deep terrestrial virosphere suggests slow motion ‘boom and burst’ cycles

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Karin Holmfeldt ◽  
Emelie Nilsson ◽  
Domenico Simone ◽  
Margarita Lopez-Fernandez ◽  
Xiaofen Wu ◽  
...  
Keyword(s):  
Antibiotic Production ◽  
Nutrient Recycling ◽  
Slow Motion ◽  
Deep Biosphere ◽  
Wide Range ◽  
Domains Of Life ◽  
Microbial Turnover ◽  
Rna Transcript ◽  
Viral Isolates ◽  
Antagonistic Interactions

AbstractThe deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in ‘metabolic standby’. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of ‘kill-the-winner’ oscillations creating slow motion ‘boom and burst’ cycles.

scholarly journals Specialized Metabolites from Ribosome Engineered Strains of Streptomyces clavuligerus

Metabolites ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 239
Author(s):  
Arshad Ali Shaikh ◽  
Louis-Felix Nothias ◽  
Santosh K. Srivastava ◽  
Pieter C. Dorrestein ◽  
Kapil Tahlan
Keyword(s):  
In Silico Analysis ◽  
Cost Effective ◽  
Gene Clusters ◽  
Streptomyces Clavuligerus ◽  
Strain Engineering ◽  
Ribosome Recycling Factor ◽  
Metabolic Potential ◽  
Putative Gene ◽  
Specialized Metabolites ◽  
Streptomyces Spp

Bacterial specialized metabolites are of immense importance because of their medicinal, industrial, and agricultural applications. Streptomyces clavuligerus is a known producer of such compounds; however, much of its metabolic potential remains unknown, as many associated biosynthetic gene clusters are silent or expressed at low levels. The overexpression of ribosome recycling factor (frr) and ribosome engineering (induced rpsL mutations) in other Streptomyces spp. has been reported to increase the production of known specialized metabolites. Therefore, we used an overexpression strategy in combination with untargeted metabolomics, molecular networking, and in silico analysis to annotate 28 metabolites in the current study, which have not been reported previously in S. clavuligerus. Many of the newly described metabolites are commonly found in plants, further alluding to the ability of S. clavuligerus to produce such compounds under specific conditions. In addition, the manipulation of frr and rpsL led to different metabolite production profiles in most cases. Known and putative gene clusters associated with the production of the observed compounds are also discussed. This work suggests that the combination of traditional strain engineering and recently developed metabolomics technologies together can provide rapid and cost-effective strategies to further speed up the discovery of novel natural products.

scholarly journals Biosignatures of ancient microbial life are present across the igneous crust of the Fennoscandian shield

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Henrik Drake ◽  
Nick M. W. Roberts ◽  
Manuel Reinhardt ◽  
Martin Whitehouse ◽  
Magnus Ivarsson ◽  
...  
Keyword(s):  
Fennoscandian Shield ◽  
Stable Carbon ◽  
Deep Biosphere ◽  
Isotopic Signatures ◽  
Microbial Life ◽  
Carbon Isotopic ◽  
Terrestrial Life ◽  
Vein Mineral ◽  
Methyl Branched Fatty Acids

AbstractEarth’s crust contains a substantial proportion of global biomass, hosting microbial life up to several kilometers depth. Yet, knowledge of the evolution and extent of life in this environment remains elusive and patchy. Here we present isotopic, molecular and morphological signatures for deep ancient life in vein mineral specimens from mines distributed across the Precambrian Fennoscandian shield. Stable carbon isotopic signatures of calcite indicate microbial methanogenesis. In addition, sulfur isotope variability in pyrite, supported by stable carbon isotopic signatures of methyl-branched fatty acids, suggest subsequent bacterial sulfate reduction. Carbonate geochronology constrains the timing of these processes to the Cenozoic. We suggest that signatures of an ancient deep biosphere and long-term microbial activity are present throughout this shield. We suggest that microbes may have been active in the continental igneous crust over geological timescales, and that subsurface investigations may be valuable in the search for extra-terrestrial life.

scholarly journals Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy)

2021 ◽  
Vol 9 (4) ◽  
pp. 859
Author(s):  
Andrea Firrincieli ◽  
Andrea Negroni ◽  
Giulio Zanaroli ◽  
Martina Cappelletti
Keyword(s):  
Archaeal Community ◽  
Hydrocarbon Biodegradation ◽  
Natural Ecosystems ◽  
Central Mediterranean ◽  
Metabolic Potential ◽  
Metabolic Role ◽  
Sequencing Studies ◽  
Terrestrial Environments ◽  
Metagenome Sequencing ◽  
Aliphatic And Aromatic Hydrocarbons

Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons.

scholarly journals The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2139
Author(s):  
Feilong Deng ◽  
Yushan Li ◽  
Yunjuan Peng ◽  
Xiaoyuan Wei ◽  
Xiaofan Wang ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Antibiotic Resistance Genes ◽  
Alpha Diversity ◽  
Distance Matrix ◽  
Archaeal Community ◽  
Gene Families ◽  
Shannon Index ◽  
Metabolic Potential ◽  
Substantial Progress ◽  
Archaeal Communities

Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray–Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

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