scholarly journals Cryptic roles of tetrathionate in the sulfur cycle of marine sediments: microbial drivers and indicators

2020 ◽  
Vol 17 (18) ◽  
pp. 4611-4631 ◽  
Author(s):  
Subhrangshu Mandal ◽  
Sabyasachi Bhattacharya ◽  
Chayan Roy ◽  
Moidu Jameela Rameez ◽  
Jagannath Sarkar ◽  
...  
Keyword(s):  
Sediment Cores ◽  
Sulfur Cycle ◽  
Growth Media ◽  
Pore Waters ◽  
Bacterial Populations ◽  
Metagenome Analysis ◽  
Minimum Zone ◽  
Chemolithotrophic Bacteria

Abstract. To explore the potential role of tetrathionate in the sedimentary sulfur cycle, population ecology of microorganisms capable of metabolizing this polythionate was revealed at 15–30 cm resolution along two, ∼3 m long, cores collected from 530 and 580 m below the sea level, off India's west coast, within the oxygen minimum zone (OMZ) of the Arabian Sea. Metagenome analysis along the cores revealed widespread occurrence of genes involved in the formation, oxidation, and reduction of tetrathionate; high diversity and relative abundance were also detected for bacteria that are known to render these metabolisms in vitro. Results of slurry culture of the sediment samples in thiosulfate- or tetrathionate-containing microbial growth media, data obtained via pure-culture isolation, and finally metatranscriptome analyses corroborated the in situ functionality of the tetrathionate-forming, tetrathionate-oxidizing, and tetrathionate-reducing microorganisms. Ion chromatography of pore waters revealed the presence of up to 11.1 µM thiosulfate in the two cores, whereas tetrathionate remained undetected in spectroscopic assay based on its reaction with cyanide. While thiosulfate oxidation by chemolithotrophic bacteria prevalent in situ is the apparent source of tetrathionate in this ecosystem, high biochemical and geochemical reactivity of this polythionate could be instrumental in its cryptic status in the sulfur cycle. Potential abiotic origin of tetrathionate in the sediment horizon explored could neither be ruled out nor confirmed from the geochemical information available. On the other hand, tetrathionate potentially present in the system can be either oxidized to sulfate or reduced back to thiosulfate/sulfide via chemolithotrophic oxidation and respiration by native bacterial populations, respectively. Up to 2.01 mM sulfide present in the sediment cores may also reduce tetrathionate abiotically to thiosulfate and elemental sulfur. However, in the absence of measured data for O2 or other oxyanions having possibilities of serving as electron acceptors, the biogeochemical modalities of the oxidative half of the tetrathionate cycle remained unresolved.

scholarly journals Cryptic role of tetrathionate in the sulfur cycle: A study from Arabian Sea sediments

2019 ◽  
Author(s):  
Subhrangshu Mandal ◽  
Sabyasachi Bhattacharya ◽  
Chayan Roy ◽  
Moidu Jameela Rameez ◽  
Jagannath Sarkar ◽  
...  
Keyword(s):  
Arabian Sea ◽  
Sediment Cores ◽  
Sulfur Cycle ◽  
Sediment Surface ◽  
Growth Media ◽  
Metagenome Analysis ◽  
Geochemical Analyses

Abstract. To explore the potential role of tetrathionate in the sulfur cycle of marine sediments, population ecology of microorganisms capable of metabolizing this polythionate was revealed at 15–30 cm resolution along two, ~ 3-m-long, cores collected from 530 and 580 meters below the sea level, off India's west coast, within the oxygen minimum zone (OMZ) of the Arabian Sea. Metagenome analysis along the two sediment-cores revealed widespread occurrence of genes involved in microbial formation, oxidation, and reduction of tetrathionate; high diversity and relative-abundance was also detected for bacteria that are known to render these metabolisms in vitro. Results of slurry-incubation of the sediment-samples in thiosulfate- or tetrathionate-containing microbial growth media, data obtained via pure-culture isolation, and finally metatranscriptome analyses, corroborated the in situ functionality of tetrathionate-forming, oxidizing, and reducing microorganisms. Geochemical analyses revealed the presence of up to 11.1 µM thiosulfate along the two cores, except a few sample-sites near the sediment-surface. Thiosulfate oxidation by chemolithotrophic bacteria prevalent in situ is the apparent source of tetrathionate in this ecosystem. However, potential abiotic origin of the polythionate can neither be ruled out nor confirmed from the geochemical information currently available for this territory. Tetrathionate, in turn, can be either oxidized to sulfate (via oxidation by the chemolithotrophs present) or reduced back to thiosulfate (via respiration by native bacteria). Up to 2.01 mM sulfide present in the sediment-cores may also reduce tetrathionate abiotically to thiosulfate and elemental sulfur. As tetrathionate was not detected in situ, high microbiological and geochemical reactivity of this polythionate was hypothesized to be instrumental in its cryptic status as a central sulfur cycle intermediate.

scholarly journals Cryptic role of tetrathionate in the sulfur cycle: A study from Arabian Sea oxygen minimum zone sediments

2019 ◽  
Author(s):  
Subhrangshu Mandal ◽  
Sabyasachi Bhattacharya ◽  
Chayan Roy ◽  
Moidu Jameela Rameez ◽  
Jagannath Sarkar ◽  
...  
Keyword(s):  
Arabian Sea ◽  
Potential Role ◽  
Sediment Cores ◽  
Oxygen Minimum Zone ◽  
Sulfur Cycle ◽  
Metagenome Analysis ◽  
Minimum Zone ◽  
Oxygen Minimum

ABSTRACTTo explore the potential role of tetrathionate in the sulfur cycle of marine sediments, the population ecology of tetrathionate-forming, oxidizing, and respiring microorganisms was revealed at 15-30 cm resolution along two, ∼3-m-long, cores collected from 530- and 580-mbsl water-depths of Arabian Sea, off India’s west coast, within the oxygen minimum zone (OMZ). Metagenome analysis along the two sediment-cores revealed widespread occurrence of the structural genes that govern these metabolisms; high diversity and relative-abundance was also detected for the bacteria known to render these processes. Slurry-incubation of the sediment-samples, pure-culture isolation, and metatranscriptome analysis, corroborated thein situfunctionality of all the three metabolic-types. Geochemical analyses revealed thiosulfate (0-11.1 μM), pyrite (0.05-1.09 wt %), iron (9232-17234 ppm) and manganese (71-172 ppm) along the two sediment-cores. Pyrites (via abiotic reaction with MnO2) and thiosulfate (via oxidation by chemolithotrophic bacteria prevalentin situ) are apparently the main sources of tetrathionate in this ecosystem. Tetrathionate, in turn, can be either converted to sulfate (via oxidation by the chemolithotrophs present) or reduced back to thiosulfate (via respiration by native bacteria); 0-2.01 mM sulfide present in the sediment-cores may also reduce tetrathionate abiotically to thiosulfate and elemental sulfur. Notably tetrathionate was not detectedin situ- high microbiological and geochemical reactivity of this polythionate is apparently instrumental in the cryptic nature of its potential role as a central sulfur cycle intermediate. Biogeochemical roles of this polythionate, albeit revealed here in the context of OMZ sediments, may well extend to the sulfur cycles of other geomicrobiologically-distinct marine sediment horizons.

scholarly journals Cryptic role of tetrathionate in the sulfur cycle: A study from Arabian Sea oxygen minimum zone sediments

2019 ◽  
Author(s):  
Subhrangshu Mandal ◽  
Sabyasachi Bhattacharya ◽  
Chayan Roy ◽  
Moidu Jameela Rameez ◽  
Jagannath Sarkar ◽  
...  
Keyword(s):  
Arabian Sea ◽  
Potential Role ◽  
Sediment Cores ◽  
Oxygen Minimum Zone ◽  
Sulfur Cycle ◽  
Metagenome Analysis ◽  
Minimum Zone ◽  
Oxygen Minimum

Abstract. To explore the potential role of tetrathionate in the sulfur cycle of marine sediments, the population ecology of tetrathionate-forming, oxidizing, and respiring microorganisms was revealed at 15–30 cm resolution along two, ~ 3-m-long, cores collected from 530- and 580-mbsl water-depths of Arabian Sea, off India’s west coast, within the oxygen minimum zone (OMZ). Metagenome analysis along the two sediment-cores revealed widespread occurrence of the structural genes that govern these metabolisms; high diversity and relative-abundance was also detected for the bacteria known to render these processes. Slurry-incubation of the sediment-samples, pure-culture isolation, and metatranscriptome analysis, corroborated the in situ functionality of all the three metabolic-types. Geochemical analyses revealed thiosulfate (0–11.1 µM), pyrite (0.05–1.09 wt %), iron (9232–17234 ppm) and manganese (71–172 ppm) along the two sediment-cores. Pyrites (via abiotic reaction with MnO2) and thiosulfate (via oxidation by chemolithotrophic bacteria prevalent in situ) are apparently the main sources of tetrathionate in this ecosystem. Tetrathionate, in turn, can be either converted to sulfate (via oxidation by the chemolithotrophs present) or reduced back to thiosulfate (via respiration by native bacteria); 0–2.01 mM sulfide present in the sediment-cores may also reduce tetrathionate abiotically to thiosulfate and elemental sulfur. Notably tetrathionate was not detected in situ – high microbiological and geochemical reactivity of this polythionate is apparently instrumental in the cryptic nature of its potential role as a central sulfur cycle intermediate. Biogeochemical roles of this polythionate, albeit revealed here in the context of OMZ sediments, may well extend to the sulfur cycles of other geomicrobiologically-distinct marine sediment horizons.

scholarly journals Long-term conservation of potato genetic resources: Methods and status of conservation

2019 ◽  
pp. 717-725
Author(s):  
Jane Muthoni ◽  
Hussein Shimelis ◽  
Rob Melis
Keyword(s):  
Genetic Resources ◽  
Slow Growth ◽  
Plant Genetic Resources ◽  
Ex Situ ◽  
Growth Media ◽  
Medium Term ◽  
Natural Habitats

Plant genetic resources (PGRs) play an important role in agriculture, environment protection, cultural property and trade; they need to be conserved. There are two fundamental approaches for the conservation of PGRs: in situ and ex situ. In situ conservation is the conservation of ecosystems and natural habitats and the maintenance and recovery of viable populations of species in their natural surroundings. Ex situ preservation is the storage of seeds or plant materials under artificial conditions to maintain their long term viability and availability for use. Genebanks employ seed storage, field collections of living plants and in vitro storage (tissue culture or cryopreservation) for ex situ preservation of PGR. Storage of orthodox seeds, which are tolerant to low moisture content and low temperatures at appropriate temperature and humidity, is the most convenient ex situ conservation method. Plants that produce recalcitrant seeds or non-viable seeds are conserved in field genebanks as well as in-vitro in slow growth media for short-to-medium term and cryopreservation in liquid nitrogen at -1960C for long-term periods. Cryopreservation is very expensive and needs trained personnel; this could explain why this method is rarely used for conservation of plant genetic resources in most developing countries. Potato tubers are bulky and highly perishable; the crop is generally conserved as clones either in field genebanks (with annual replanting), in-vitro conservation in slow growth media for short-to-medium term and cryopreservation for long term. Field genebanks are expensive to maintain and the crop is exposed to many dangers; hence, cryopreservation is the only feasible method for long term conservation. However, given the high cost of cryopreservation, long-term conservation of potato genetic resources is poorly developed in most resource-poor countries leading to high rates of genetic erosion. This paper looks into the various methods that that can be applied to conserve potato genetic resources and the status of conservation of potatoes in major genebanks and some countries.

scholarly journals Persistent colonization of non-lymphoid tissue-resident macrophages by Stenotrophomonas maltophilia

2019 ◽  
Author(s):  
Ichiro Takahashi ◽  
Koji Hosomi ◽  
Takahiro Nagatake ◽  
Hirokazu Tobou ◽  
Daiki Yamamoto ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Dendritic Cells ◽  
16S Rrna ◽  
Mitochondrial Respiration ◽  
Lymphoid Tissue ◽  
Stenotrophomonas Maltophilia ◽  
Commensal Bacteria ◽  
Metagenome Analysis

Abstract Accumulating evidence has revealed that lymphoid-tissue-resident commensal bacteria (e.g., Alcaligenes spp.) survive within dendritic cells. We extended our previous study by investigating microbes that persistently colonize colonic macrophages. 16S rRNA-based metagenome analysis using DNA purified from murine colonic macrophages revealed the presence of Stenotrophomonas maltophilia. The in situ intracellular colonization by S. maltophilia was recapitulated in vitro by using bone marrow-derived macrophages (BMDMs). Co-culture of BMDMs with clinically isolated S. maltophilia led to increased mitochondrial respiration and robust IL-10 production. We further identified a 25-kDa protein encoded by the gene assigned as smlt2713 (recently renamed as SMLT_RS12935) and secreted by S. maltophilia as the factor responsible for enhanced IL-10 production by BMDMs. IL-10 production is critical for maintenance of the symbiotic condition, because intracellular colonization by S. maltophilia was impaired in IL-10-deficient BMDMs, and smlt2713-deficient S. maltophilia failed to persistently colonize IL-10-competent BMDMs. These findings indicate a novel commensal network between colonic macrophages and S. maltophilia that is mediated by IL-10 and smlt2713.

scholarly journals Microbial activity, methane production, and carbon storage in Early Holocene North Sea peats

2020 ◽  
Author(s):  
Tanya J. R. Lippmann ◽  
Michiel H. in 't Zandt ◽  
Nathalie N. L. Van der Putten ◽  
Freek S. Busschers ◽  
Marc P. Hijma ◽  
...  
Keyword(s):  
North Sea ◽  
Carbon Sources ◽  
Methanogenic Archaea ◽  
Molecular Signatures ◽  
Pore Waters ◽  
Bacterial Populations ◽  
The North ◽  
Peat Deposits ◽  
Micro Organisms

Abstract. Northern latitude peatlands act as important carbon sources and sinks but little is known about the greenhouse gas (GHG) budget of peatlands submerged beneath the North Sea during the last glacial-interglacial transition. We found that whilst peat formation was diachronous, commencing between 13,680 and 8,360 calibrated years before the present, stratigraphic layering and local vegetation succession were consistent across a large study area. The CH4 concentrations of the sediment pore waters were low at most sites, with the exception of two locations, and the stored carbon was large. Incubation experiments in the laboratory revealed molecular signatures of methanogenic archaea, with strong increases in rates of activity upon methylated substrate amendment. Remarkably, methanotrophic activity and the respective diagnostic molecular signatures could be not be detected. Heterotrophic Bathyarchaeia dominated the archaeal communities and bacterial populations were dominated by candidate phylum JS1 bacteria. Although CH4 accumulation is low at most sites, the presence of in situ methanogenic micro-organisms, the absence of methanotrophy, and large widespread stores of carbon hold the potential for GHG production if catalysed by a change in environmental conditions. Despite being earmarked as a critical source of CH4 seepage, seepage from these basal-peat deposits is restricted, as evidenced by low in situ CH4 concentrations.

scholarly journals Microbial activity, methane production, and carbon storage in Early Holocene North Sea peats

2021 ◽  
Vol 18 (19) ◽  
pp. 5491-5511
Author(s):  
Tanya J. R. Lippmann ◽  
Michiel H. in 't Zandt ◽  
Nathalie N. L. Van der Putten ◽  
Freek S. Busschers ◽  
Marc P. Hijma ◽  
...  
Keyword(s):  
North Sea ◽  
Carbon Sources ◽  
Methanogenic Archaea ◽  
Molecular Signatures ◽  
Pore Waters ◽  
Bacterial Populations ◽  
The North ◽  
Ch4 Production ◽  
Carbon Stores

Abstract. Northern latitude peatlands act as important carbon sources and sinks, but little is known about the greenhouse gas (GHG) budgets of peatlands that were submerged beneath the North Sea during the last glacial–interglacial transition. We found that whilst peat formation was diachronous, commencing between 13 680 and 8360 calibrated years before the present, stratigraphic layering and local vegetation succession were consistent across a large study area. Large carbon stores were measured. In situ methane (CH4) concentrations of sediment pore waters were widespread but low at most sites, with the exception of two locations. Incubation experiments in the laboratory revealed molecular signatures of methanogenic archaea, with strong increases in rates of activity upon methylated substrate amendment. Remarkably, methanotrophic activity and the respective diagnostic molecular signatures could not be detected. Heterotrophic Bathyarchaeota dominated the archaeal communities, and bacterial populations were dominated by candidate phylum JS1 bacteria. In the absence of active methanogenic microorganisms, we conclude that these sediment harbour low concentrations of widespread millennia-old CH4. The presence of large widespread stores of carbon and in situ methanogenic microorganisms, in the absence of methanotrophic microorganisms, holds the potential for microbial CH4 production if catalysed by a change in environmental conditions.

Development of a fermentation system to model sessile bacterial populations in the human colon

Biofilms ◽  
2004 ◽  
Vol 1 (1) ◽  
pp. 13-19 ◽  
Author(s):  
H. M. Probert ◽  
G. R. Gibson
Keyword(s):  
Culture Fluid ◽  
Human Colon ◽  
Healthy Human ◽  
Bacterial Populations ◽  
Fermentation System ◽  
Colonic Microflora ◽  
Osmotic Effect ◽  
Planktonic Bacteria

A fermentation system was designed to model the human colonic microflora in vitro. The system provided a framework of mucin beads to encourage the adhesion of bacteria, which was encased within a dialysis membrane. The void between the beads was inoculated with faeces from human donors. Water and metabolites were removed from the fermentation by osmosis using a solution of polyethylene glycol (PEG). The system was concomitantly inoculated alongside a conventional single-stage chemostat. Three fermentations were carried out using inocula from three healthy human donors.Bacterial populations from the chemostat and biofilm system were enumerated using fluorescence in situ hybridization. The culture fluid was also analysed for its short-chain fatty acid (SCFA) content. A higher cell density was achieved in the biofilm fermentation system (taking into account the contribution made by the bead-associated bacteria) as compared with the chemostat, owing to the removal of water and metabolites. Evaluation of the bacterial populations revealed that the biofilm system was able to support two distinct groups of bacteria: bacteria growing in association with the mucin beads and planktonic bacteria in the culture fluid. Furthermore, distinct differences were observed between populations in the biofilm fermenter system and the chemostat, with the former supporting higher populations of clostridia and Escherichia coli. SCFA levels were lower in the biofilm system than in the chemostat, as in the former they were removed via the osmotic effect of the PEG. These experiments demonstrated the potential usefulness of the biofilm system for investigating the complexity of the human colonic microflora and the contribution made by sessile bacterial populations.

Preliminary Analysis of the Lipase Gene (gehM ) Expression of Staphylococcus xylosus In Vitro and during Fermentation of Naturally Fermented Sausages (In Situ)

2007 ◽  
Vol 70 (11) ◽  
pp. 2665-2669 ◽  
Author(s):  
LUCILLA IACUMIN ◽  
LUCA COCOLIN ◽  
CARLO CANTONI ◽  
GIUSEPPE COMI
Keyword(s):  
Gene Expression ◽  
Preliminary Analysis ◽  
Short Chain Fatty Acids ◽  
Growth Media ◽  
Lipase Gene ◽  
Fermented Sausage ◽  
Staphylococcus Xylosus ◽  
Fermented Sausages

Coagulase-negative catalase-positive cocci (CNCPC) play a very important role during the fermentation of sausages. In particular, they are involved in the aroma formation of the final product, because they release lipases that are able to free short-chain fatty acids that are contributing to the sensory characteristics of the fermented sausage. Few studies have been undertaken to elucidate the regulation of lipase gene expression in Staphylococcus xylosus by substrate molecules or products of lipolysis. The aim of this study was to analyze the gehM gene expression of S. xylosus DSMZ 6179 in vitro with growth media containing different concentrations of lipids and in situ during the maturation of fermented sausages. The results obtained suggest that a concentration that increases in triglycerides in the growth medium suppresses the expression of the lipase gene.

Substrata effects on bacterial biofilm development in a subsurface flow dairy waste treatment wetland

2003 ◽  
Vol 48 (8) ◽  
pp. 261-269 ◽  
Author(s):  
G. Silyn-Roberts ◽  
G. Lewis
Keyword(s):  
Population Structure ◽  
In Situ Hybridisation ◽  
Treatment Wetland ◽  
Bacterial Populations ◽  
Rock Types ◽  
Bacterial Adsorption ◽  
Adsorption Rates ◽  
Biofilm Development

Biofilm development on two distinct rock substrata was investigated both in vitro and in a subsurface flow wastewater treatment wetland in order to determine the effect of hydrophobicity on initial bacterial adsorption, tertiary biofilm development and microbial population structure. Two commonly used wetland rock types, slag (a hydrophobic by-product of the steel smelter industry) and greywacke (a more hydrophilic sedimentary rock) were evaluated. In vitro investigations of initial microbial adsorption trends showed that the more hydrophobic slag displayed rapid bacterial adsorption rates compared to greywacke. Mean microbial adsorption rates of a mixed wetland bacterial population over 5 hours, described using a first order kinetics model, were 1.3 × 10-12 m/sec for slag and consistently lower at 8.7 × 10-13 m/sec for greywacke. Pristine rock studs of the two substrata were also exposed to wetland microbial communities during a six week field trial using confocal scanning laser microscopy to determine tertiary biofilm structure and fluorescent in situ hybridisation to investigate bacterial populations. During the first five weeks of growth CSLM analysis revealed that 75% of biofilms on slag were thicker and had greater coverage compared with those grown on greywacke. After six weeks of growth over 50% of the tertiary biofilms were structurally very similar on both rock types and only 25% of those grown on slag were larger than those on greywacke. In situ hybridisation analysis of bacterial populations revealed very little difference in population structure between biofilms grown on slag and those grown on greywacke. Eubacteria were present as a very high proportion of total bacteria throughout biofilm development (74.3%). The beta subgroup was the most populous of the Proteobacteria (31.4%) followed by the gamma subgroup (13.4%)and the alpha subgroup (1.3%). The results of this study suggest that slag, as a more hydrophobic substratum, promotes the initial adsorption of bacteria during early biofilm growth and better supports mature biofilm structures when used in wetlands. This study has implications for the design and construction of wastewater treatment wetlands.

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