Procaryotic Diversity and Hydrogenotrophic Methanogenesis in an Alkaline Spring (La Crouen, New Caledonia)

(1) Background: The geothermal spring of La Crouen (New Caledonia) discharges warm (42 °C) alkaline water (pH~9) enriched in dissolved nitrogen with traces of methane, but its microbial diversity has not yet been studied. (2) Methods: Cultivation-dependent and -independent methods (e.g., Illumina sequencing and quantitative PCR based on 16S rRNA gene) were used to describe the prokaryotic diversity of this spring. (3) Results: Prokaryotes were mainly represented by Proteobacteria (57% on average), followed by Cyanobacteria, Chlorofexi, and Candidatus Gracilibacteria (GN02/BD1-5) (each > 5%). Both potential aerobes and anaerobes, as well as mesophilic and thermophilic microorganisms, were identified. Some of them had previously been detected in continental hyperalkaline springs found in serpentinizing environments (The Cedars, Samail, Voltri, and Zambales ophiolites). Gammaproteobacteria, Ca. Gracilibacteria and Thermotogae were significantly more abundant in spring water than in sediments. Potential chemolithotrophs mainly included beta- and gammaproteobacterial genera of sulfate-reducers (Ca. Desulfobacillus), methylotrophs (Methyloversatilis), sulfur-oxidizers (Thiofaba, Thiovirga), or hydrogen-oxidizers (Hydrogenophaga). Methanogens (Methanobacteriales and Methanosarcinales) were the dominant Archaea, as found in serpentinization-driven and deep subsurface ecosystems. A novel alkaliphilic hydrogenotrophic methanogen (strain CAN) belonging to the genus Methanobacterium was isolated, suggesting that hydrogenotrophic methanogenesis occurs at La Crouen.

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Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

Frontiers in Microbiology ◽

10.3389/fmicb.2021.668240 ◽

2021 ◽

Vol 12 ◽

Author(s):

Charles S. Cockell ◽

Bettina Schaefer ◽

Cornelia Wuchter ◽

Marco J. L. Coolen ◽

Kliti Grice ◽

...

Keyword(s):

Microbial Communities ◽

Amplicon Sequencing ◽

Granitic Rocks ◽

Rrna Gene ◽

Deep Biosphere ◽

Deep Subsurface ◽

Cell Biomass ◽

Colonization Potential ◽

The Impact

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

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Sinking particles promote vertical connectivity in the ocean microbiome

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1802470115 ◽

2018 ◽

Vol 115 (29) ◽

pp. E6799-E6807 ◽

Cited By ~ 48

Author(s):

Mireia Mestre ◽

Clara Ruiz-González ◽

Ramiro Logares ◽

Carlos M. Duarte ◽

Josep M. Gasol ◽

...

Keyword(s):

Surface Waters ◽

Deep Ocean ◽

Rrna Gene ◽

Carbon Export ◽

Size Fractions ◽

Sinking Particles ◽

Prokaryotic Diversity ◽

Compositional Variability ◽

Organic Particles ◽

Community Connectivity

The sinking of organic particles formed in the photic layer is a main vector of carbon export into the deep ocean. Although sinking particles are heavily colonized by microbes, so far it has not been explored whether this process plays a role in transferring prokaryotic diversity from surface to deep oceanic layers. Using Illumina sequencing of the 16S rRNA gene, we explore here the vertical connectivity of the ocean microbiome by characterizing marine prokaryotic communities associated with five different size fractions and examining their compositional variability from surface down to 4,000 m across eight stations sampled in the Atlantic, Pacific, and Indian Oceans during the Malaspina 2010 Expedition. Our results show that the most abundant prokaryotes in the deep ocean are also present in surface waters. This vertical community connectivity seems to occur predominantly through the largest particles because communities in the largest size fractions showed the highest taxonomic similarity throughout the water column, whereas free-living communities were more isolated vertically. Our results further suggest that particle colonization processes occurring in surface waters determine to some extent the composition and biogeography of bathypelagic communities. Overall, we postulate that sinking particles function as vectors that inoculate viable particle-attached surface microbes into the deep-sea realm, determining to a considerable extent the structure, functioning, and biogeography of deep ocean communities.

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Methanospirillum psychrodurum sp. nov., isolated from wetland soil

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.057299-0 ◽

2014 ◽

Vol 64 (Pt_2) ◽

pp. 638-641 ◽

Cited By ~ 26

Author(s):

Liguang Zhou ◽

Xiaoli Liu ◽

Xiuzhu Dong

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Sequence Similarity ◽

Wetland Soil ◽

Rrna Gene ◽

Lower Growth ◽

Content Type ◽

Link Type ◽

Hydrogenotrophic Methanogenesis

A psychrotolerant methanogenic strain, X-18T, was isolated from the soil of the Madoi wetland at Qinghai, Tibetan plateau, China. Cells were wavy rods (11–62 µm long) with blunt tapered ends and Gram-stain-negative. Strain X-18T grew strictly anaerobically and produced methane exclusively from H2/CO2. Growth occurred in the temperature range of 4–32 °C and optimally at 25 °C. Growth pH ranged from 6.5 to 8.0 and the optimum was 7.0. The G+C content of the genomic DNA of strain X-18T was 44.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and the alpha subunit of methyl-coenzyme M reductase indicated that strain X-18T was affiliated to the genus Methanospirillum and was most closely related to Methanospirillum lacunae Ki8-1T, with 96.3 % 16S rRNA gene sequence similarity. However, strain X-18T could be distinguished from the existing species of the genus Methanospirillum by its lower growth temperature and obligate hydrogenotrophic methanogenesis. On the basis of phenotypic characteristics and phylogenetic analysis, strain X-18T represents a novel species of the genus Methanospirillum , for which the name Methanospirillum psychrodurum sp. nov. is proposed and strain X-18T is assigned as the type strain ( = CGMCC 1.5186T = JCM 19216T).

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Metagenomic data on prokaryotic diversity of Kunashir island geothermal spring

Data in Brief ◽

10.1016/j.dib.2020.106244 ◽

2020 ◽

Vol 32 ◽

pp. 106244

Author(s):

Alexei S. Rozanov ◽

Anton V. Korzhuk ◽

Valeria N. Shlyakhtun ◽

Aleksandra A. Shipova ◽

Sergey E. Peltek

Keyword(s):

Metagenomic Data ◽

Geothermal Spring ◽

Prokaryotic Diversity ◽

Kunashir Island

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Gracilibacter thermotolerans gen. nov., sp. nov., an anaerobic, thermotolerant bacterium from a constructed wetland receiving acid sulfate water

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64040-0 ◽

2006 ◽

Vol 56 (9) ◽

pp. 2089-2093 ◽

Cited By ~ 44

Author(s):

Yong-Jin Lee ◽

Christopher S. Romanek ◽

Gary L. Mills ◽

Richard C. Davis ◽

William B. Whitman ◽

...

Keyword(s):

Constructed Wetland ◽

Phylogenetic Trees ◽

Sequence Similarity ◽

Salinity Range ◽

Rrna Gene ◽

Acid Sulfate ◽

Water Ph ◽

Bacterium Strain ◽

Branched Chain ◽

Thermotolerant Bacterium

An obligatorily anaerobic, thermotolerant, asporogenic bacterium, strain JW/YJL-S1T, was isolated from a sediment sample of a constructed wetland system receiving acid sulfate water (pH 1.6–3.0). Cells of strain JW/YJL-S1T were straight to curved rods 0.2–0.4 μm in diameter and 2.0–7.0 μm in length, and stained Gram-negative. Growth of strain JW/YJL-S1T was observed at 25–54 °C (no growth at or below 20 or at or above 58 °C), with an optimum temperature range for growth of 42.5–46.5 °C. The pH25 °C range for growth was 6.0–8.25 (no growth at or below pH 5.7 or at or above pH 8.5), with optimum growth at pH 6.8–7.75. The salinity range for growth was 0–1.5 % (w/v) NaCl, with an optimum at 0–0.5 %. During growth on glucose the isolate produced acetate, lactate and ethanol as main fermentation end products. The fatty acid composition was dominated by branched-chain compounds: i15 : 0, a15 : 0, i16 : 0 and i17 : 0. The G+C content of the genomic DNA was 42.8 mol% (HPLC). Strain JW/YJL-S1T showed polymorphism of the 16S rRNA gene. Its closest relative was the thermophilic Clostridium thermosuccinogenes DSM 5807T (a member of Clostridium cluster III) (a blastn search revealed Clostridium pascui DSM 10365T to have 92.7 % gene sequence similarity, the highest value). The inferred phylogenetic trees placed strain JW/YJL-S1T between Clostridium clusters I/II and III. Based on the morphological and phylogenetic data presented, JW/YJL-S1T (=DSM 17427T=ATCC BAA-1219T) is proposed as the type strain of a novel species in a new genus, Gracilibacter thermotolerans gen. nov., sp. nov.

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Isolation and Characterization of Methanothermobacter crinale sp. nov., a Novel Hydrogenotrophic Methanogen from the Shengli Oil Field

Applied and Environmental Microbiology ◽

10.1128/aem.00210-11 ◽

2011 ◽

Vol 77 (15) ◽

pp. 5212-5219 ◽

Cited By ~ 67

Author(s):

Lei Cheng ◽

Lirong Dai ◽

Xia Li ◽

Hui Zhang ◽

Yahai Lu

Keyword(s):

Oil Sands ◽

Type Strain ◽

High Performance ◽

Sequence Similarity ◽

Oil Field ◽

Rrna Gene ◽

Content Type ◽

Chromatography Analysis ◽

Hydrogenotrophic Methanogenesis ◽

Isolation And Characterization

ABSTRACTSyntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis is an alternative methanogenic pathway in certain thermophilic anaerobic environments such as high-temperature oil reservoirs and thermophilic biogas reactors. In these environments, the dominant thermophilic methanogens were generally related to uncultured organisms of the genusMethanothermobacter. Here we isolated two representative strains, Tm2Tand HMD, from the oil sands and oil production water in the Shengli oil field in the People's Republic of China. The type strain, Tm2T, was nonmotile and stained Gram positive. The cells were straight to slightly curved rods (0.3 μm in width and 2.2 to 5.9 μm in length), but some of them possessed a coccal shape connecting with the rods at the ends. Strain Tm2Tgrew with H2-CO2, but acetate is required. Optimum growth of strain Tm2Toccurred in the presence of 0.025 g/liter NaCl at pH 6.9 and a temperature of 65°C. The G+C content of the genomic DNA was 40.1 mol% ± 1.3 mol% (by the thermal denaturation method) or 41.1 mol% (by high-performance liquid chromatography). Analysis of the 16S rRNA gene sequence indicated that Tm2Twas most closely related toMethanothermobacter thermautotrophicusΔHTandMethanothermobacter wolfeiiVKM B-1829T(both with a sequence similarity of 96.4%). Based on these phenotypic and phylogenic characteristics, a novel species was proposed and namedMethanothermobacter crinalesp. nov. The type strain is Tm2T(ACCC 00699T= JCM 17393T).

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Succession within the prokaryotic communities during the VAHINE mesocosms experiment in the New Caledonia lagoon

Biogeosciences ◽

10.5194/bg-13-2319-2016 ◽

2016 ◽

Vol 13 (8) ◽

pp. 2319-2337 ◽

Cited By ~ 12

Author(s):

Ulrike Pfreundt ◽

France Van Wambeke ◽

Mathieu Caffin ◽

Sophie Bonnet ◽

Wolfgang R. Hess

Keyword(s):

N2 Fixation ◽

Temporal Dynamics ◽

New Caledonia ◽

Abiotic Factors ◽

Niche Partitioning ◽

16S Rrna Gene Sequencing ◽

Inorganic Phosphorus ◽

Shannon Index ◽

Rrna Gene ◽

South Pacific Ocean

Abstract. N2 fixation fuels ∼  50 % of new primary production in the oligotrophic South Pacific Ocean. The VAHINE experiment has been designed to track the fate of diazotroph-derived nitrogen (DDN) and carbon within a coastal lagoon ecosystem in a comprehensive way. For this, large-volume ( ∼  50 m3) mesocosms were deployed in the New Caledonian lagoon and were intentionally fertilized with dissolved inorganic phosphorus (DIP) to stimulate N2 fixation. This study examined the temporal dynamics of the prokaryotic community together with the evolution of biogeochemical parameters for 23 consecutive days in one of these mesocosms (M1) and in the Nouméa lagoon using MiSeq 16S rRNA gene sequencing and flow cytometry. Combining these methods allowed for inference of absolute cell numbers from 16S data. We observed clear successions within M1, some of which were not mirrored in the lagoon. The dominating classes in M1 were Alpha- and Gammaproteobacteria, Cyanobacteria, eukaryotic microalgae, Marine Group II Euryarchaeota, Flavobacteriia, and Acidimicrobia. Enclosure led to significant changes in the M1 microbial community, probably initiated by the early decay of Synechococcus and diatoms. However, we did not detect a pronounced bottle effect with a copiotroph-dominated community. The fertilization with ∼  0.8 µM DIP on day 4 did not have directly observable effects on the overall community within M1, as the data samples obtained from before and 4 days after fertilization clustered together, but likely influenced the development of individual populations later on, like Defluviicoccus-related bacteria and UCYN-C-type diazotrophic cyanobacteria (Cyanothece). Growth of UCYN-C led to among the highest N2-fixation rates ever measured in this region and enhanced growth of nearly all abundant heterotrophic groups in M1. We further show that different Rhodobacteraceae were the most efficient heterotrophs in the investigated system and we observed niche partitioning within the SAR86 clade. Whereas the location in- or outside the mesocosm had a significant effect on community composition, the temporal effect was significantly stronger and similar in both locations, suggesting that overarching abiotic factors were more influential than the enclosure. While temporal community changes were evident, prokaryotic diversity (Shannon index) only declined slightly from ∼  6.5 to 5.7 or 6.05 in the lagoon and M1, respectively, throughout the experiment, highlighting the importance of multiple and varying sources of organic matter maintaining competition.

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Succession within the prokaryotic communities during the VAHINE mesocosms experiment in the New Caledonia lagoon

Biogeosciences Discussions ◽

10.5194/bgd-12-20179-2015 ◽

2015 ◽

Vol 12 (24) ◽

pp. 20179-20222 ◽

Cited By ~ 1

Author(s):

U. Pfreundt ◽

F. Van Wambeke ◽

S. Bonnet ◽

W. R. Hess

Keyword(s):

N2 Fixation ◽

Temporal Dynamics ◽

New Caledonia ◽

Abiotic Factors ◽

Niche Partitioning ◽

16S Rrna Gene Sequencing ◽

Inorganic Phosphorus ◽

Shannon Index ◽

Rrna Gene ◽

South Pacific Ocean

Abstract. N2 fixation fuels ~ 50 % of new primary production in the oligotrophic South Pacific Ocean. The VAHINE experiment has been designed to track the fate of diazotroph derived nitrogen (DDN) and carbon within a coastal lagoon ecosystem in a comprehensive way. For this, large-volume (~ 50 m3) mesocosms were deployed in the New Caledonia lagoon and were intentionally fertilized with dissolved inorganic phosphorus (DIP) to stimulate N2 fixation. This study examined the temporal dynamics of the prokaryotic community together with the evolution of biogeochemical parameters for 23 consecutive days in one of these mesocosms (M1) and in the Nouméa lagoon using MiSeq 16S rRNA gene sequencing. We observed clear successions within M1, some of which were not mirrored in the lagoon. The dominating classes in M1 were alpha- and gammaproteobacteria, cyanobacteria (mainly Synechococcus), eukaryotic microalgae, on days 10 and 14 Marine Group II euryarchaea, on days 12–23 also Flavobacteriia. Enclosure led to significant changes in the M1 microbial community, probably initiated by the early decay of Synechococcus and diatoms. However, we did not detect a pronounced bottle effect with a copiotroph-dominated community. The fertilization with ~ 0.8 μM DIP on day 4 did not have directly observable effects on the overall community within M1, as the data samples obtained from before and four days after fertilization clustered together, but likely influenced the development of individual populations later on, like Defluviicoccus-related bacteria and UCYN-C type diazotrophic cyanobacteria. Growth of UCYN-C led to among the highest N2 fixation rates ever measured in this region and enhanced growth of nearly all abundant heterotrophic groups in M1. We further show that different Rhodobacteraceae were the most efficient heterotrophs in the investigated system and we observed niche partitioning within the SAR86 clade. Whereas the location in- or outside the mesocosm had a significant effect on community composition, the temporal effect was significantly stronger and similar in both locations, suggesting that overarching abiotic factors were more influential than the enclosure. While temporal community changes were evident, prokaryotic diversity (Shannon Index) only declined slightly from ~ 6.5 to 5.7 or 6.05 in the lagoon and M1, respectively, throughout the experiment, highlighting the importance of multiple and varying sources of organic matter maintaining competition.

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16S rRNA Gene Amplicon Profiling of Anaerobic Bulking-Associated Prokaryotic Microbiota in a Mesophilic Expanded Granular Sludge Bed Reactor for Beverage Wastewater Treatment

Microbiology Resource Announcements ◽

10.1128/mra.00678-19 ◽

2019 ◽

Vol 8 (30) ◽

Cited By ~ 1

Author(s):

Takeshi Yamada ◽

Jun Harada ◽

Yuki Okazaki ◽

Tsuyoshi Yamaguchi ◽

Atsushi Nakano

Keyword(s):

Wastewater Treatment ◽

16S Rrna ◽

16S Rrna Gene ◽

Granular Sludge ◽

Rrna Gene ◽

High Quality ◽

Prokaryotic Diversity ◽

Diversity Profiles

Information regarding prokaryotic microbiota associated with anaerobic bulking is limited. Here, we provide 16S rRNA gene-based prokaryotic diversity profiles for anaerobic bulking and healthy granular sludge in a mesophilic expanded granular sludge bed (EGSB) reactor. These data were tabulated at the phylum level based on high-quality reads.

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The Rheology and Performance of Geothermal Spring Water-Based Drilling Fluids

Geofluids ◽

10.1155/2019/3786293 ◽

2019 ◽

Vol 2019 ◽

pp. 1-8 ◽

Cited By ~ 1

Author(s):

Emine Avci ◽

Bayram Ali Mert

Keyword(s):

Yield Point ◽

Elevated Temperatures ◽

Spring Water ◽

Geothermal Water ◽

Fluid Loss ◽

Water Type ◽

Drilling Mud ◽

Geothermal Spring ◽

Cake Thickness ◽

Water Based

In this study, the rheological properties and performances of mud prepared with geothermal spring water to be used by geothermal drilling operators were examined at ambient and elevated temperatures. In this context, mud samples were prepared in the compositions detailed in the API specification by using five different geothermal spring water types and a distilled water type. Afterwards, density, apparent viscosity, plastic viscosity, yield point, gel strength, fluid loss, pH, and filter cake thickness of these samples were measured. The drilling muds were analyzed by means of rheological tests in accordance with the standards of the American Petroleum Institute (API). The experimental results have revealed that the mud prepared with geothermal water have lower viscosity and yield point compared to those prepared with freshwater at elevated temperatures. The stability of the muds decreases, especially at temperatures higher than 250°F, and they start to become flocculated. It was concluded that geothermal water-based muds have higher API fluid loss and cake thickness than the freshwater-based one. Therefore, it could be interpreted that the muds prepared with geothermal spring water will exhibit lower flow performance and lower ability of hole cleaning and rate of penetration compared to the freshwater muds. Hence, it is recommended that this kind of water should not be used to prepare drilling mud.

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