scholarly journals Quantitative Transcriptomics Reveals the Growth- and Nutrient-Dependent Response of a Streamlined Marine Methylotroph to Methanol and Naturally Occurring Dissolved Organic Matter

mBio ◽  
2016 ◽  
Vol 7 (6) ◽  
Author(s):  
Scott M. Gifford ◽  
Jamie W. Becker ◽  
Oscar A. Sosa ◽  
Daniel J. Repeta ◽  
Edward F. DeLong
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Carbon Metabolism ◽  
Marine Organic Matter ◽  
Naturally Occurring ◽  
Genome Wide ◽  
Carbon Substrates ◽  
Mrna Content ◽  
Nutrient Conditions

ABSTRACT The members of the OM43 clade of Betaproteobacteria are abundant coastal methylotrophs with a range of carbon-utilizing capabilities. However, their underlying transcriptional and metabolic responses to shifting conditions or different carbon substrates remain poorly understood. We examined the transcriptional dynamics of OM43 isolate NB0046 subjected to various inorganic nutrient, vitamin, and carbon substrate regimes over different growth phases to (i) develop a quantitative model of its mRNA content; (ii) identify transcriptional markers of physiological activity, nutritional state, and carbon and energy utilization; and (iii) identify pathways involved in methanol or naturally occurring dissolved organic matter (DOM) metabolism. Quantitative transcriptomics, achieved through addition of internal RNA standards, allowed for analyses on a transcripts-per-cell scale. This streamlined bacterium exhibited substantial shifts in total mRNA content (ranging from 1,800 to 17 transcripts cell −1 in the exponential and deep stationary phases, respectively) and gene-specific transcript abundances (>1,000-fold increases in some cases), depending on the growth phase and nutrient conditions. Carbon metabolism genes exhibited substantial dynamics, including those for ribulose monophosphate, tricarboxylic acid (TCA), and proteorhodopsin, as well as methanol dehydrogenase ( xoxF ), which, while always the most abundant transcript, increased from 5 to 120 transcripts cell −1 when cultures were nutrient and vitamin amended. In the DOM treatment, upregulation of TCA cycle, methylcitrate cycle, vitamin, and organic phosphorus genes suggested a metabolic route for this complex mixture of carbon substrates. The genome-wide inventory of transcript abundances produced here provides insight into a streamlined marine bacterium’s regulation of carbon metabolism and energy flow, providing benchmarks for evaluating the activity of OM43 populations in situ . IMPORTANCE Bacteria exert a substantial influence on marine organic matter flux, yet the carbon components targeted by specific bacterial groups, as well as how those groups’ metabolic activities change under different conditions, are not well understood. Gene expression studies of model organisms can identify these responses under defined conditions, which can then be compared to environmental transcriptomes to elucidate in situ activities. This integration, however, is limited by the data’s relative nature. Here, we report the fully quantitative transcriptome of a marine bacterium, providing a genome-wide survey of cellular transcript abundances and how they change with different states of growth, nutrient conditions, and carbon substrates. The results revealed the dynamic metabolic strategies this methylotroph has for processing both simple one-carbon compounds and the complex multicarbon substrates of naturally derived marine organic matter and provide baseline quantitative data for identifying their in situ activities and impact on the marine carbon cycle.

scholarly journals Functional and Structural Responses of Hyporheic Biofilms to Varying Sources of Dissolved Organic Matter

2014 ◽  
Vol 80 (19) ◽  
pp. 6004-6012 ◽  
Author(s):  
Karoline Wagner ◽  
Mia M. Bengtsson ◽  
Katharina Besemer ◽  
Anna Sieczko ◽  
Nancy R. Burns ◽  
...  
Keyword(s):  
Organic Matter ◽  
16S Rrna ◽  
Dissolved Organic Matter ◽  
Community Composition ◽  
Hyporheic Zone ◽  
Priority Effects ◽  
Stream Ecosystems ◽  
Rrna Gene ◽  
Structural Responses

ABSTRACTHeadwater streams are tightly connected with the terrestrial milieu from which they receive deliveries of organic matter, often through the hyporheic zone, the transition between groundwater and streamwater. Dissolved organic matter (DOM) from terrestrial sources (that is, allochthonous) enters the hyporheic zone, where it may mix with DOM fromin situproduction (that is, autochthonous) and where most of the microbial activity takes place. Allochthonous DOM is typically considered resistant to microbial metabolism compared to autochthonous DOM. The composition and functioning of microbial biofilm communities in the hyporheic zone may therefore be controlled by the relative availability of allochthonous and autochthonous DOM, which can have implications for organic matter processing in stream ecosystems. Experimenting with hyporheic biofilms exposed to model allochthonous and autochthonous DOM and using 454 pyrosequencing of the 16S rRNA (targeting the “active” community composition) and of the 16S rRNA gene (targeting the “bulk” community composition), we found that allochthonous DOM may drive shifts in community composition whereas autochthonous DOM seems to affect community composition only transiently. Our results suggest that priority effects based on resource-driven stochasticity shape the community composition in the hyporheic zone. Furthermore, measurements of extracellular enzymatic activities suggest that the additions of allochthonous and autochthonous DOM had no clear effect on the function of the hyporheic biofilms, indicative of functional redundancy. Our findings unravel possible microbial mechanisms that underlie the buffering capacity of the hyporheic zone and that may confer stability to stream ecosystems.

Dissolved Organic Matter Sorption and Molecular Fractionation by Naturally Occurring Bacteriogenic Iron (Oxyhydr)oxides

2019 ◽  
Vol 53 (8) ◽  
pp. 4295-4304 ◽  
Author(s):  
Tyler D. Sowers ◽  
Kathryn L. Holden ◽  
Elizabeth K. Coward ◽  
Donald L. Sparks
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Naturally Occurring ◽  
Molecular Fractionation

Insights into the nature of cometary organic matter from terrestrial analogues

2012 ◽  
Vol 11 (2) ◽  
pp. 83-92 ◽  
Author(s):  
Richard W. Court ◽  
Mark A. Sephton
Keyword(s):  
Organic Matter ◽  
Cometary Nucleus ◽  
Cometary Nuclei ◽  
Naturally Occurring ◽  
Polycyclic Aromatic ◽  
Radiation Induced ◽  
Remote Observation ◽  
Complex Organic ◽  
Cometary Comae

AbstractThe nature of cometary organic matter is of great interest to investigations involving the formation and distribution of organic matter relevant to the origin of life. We have used pyrolysis–Fourier transform infrared (FTIR) spectroscopy to investigate the chemical effects of the irradiation of naturally occurring bitumens, and to relate their products of pyrolysis to their parent assemblages. The information acquired has then been applied to the complex organic matter present in cometary nuclei and comae. Amalgamating the FTIR data presented here with data from published studies enables the inference of other comprehensive trends within hydrocarbon mixtures as they are progressively irradiated in a cometary environment, namely the polymerization of lower molecular weight compounds; an increased abundance of polycyclic aromatic hydrocarbon structures; enrichment in 13C; reduction in atomic H/C ratio; elevation of atomic O/C ratio and increase in the temperature required for thermal degradation. The dark carbonaceous surface of a cometary nucleus will display extreme levels of these features, relative to the nucleus interior, while material in the coma will reflect the degree of irradiation experienced by its source location in the nucleus. Cometary comae with high methane/water ratios indicate a nucleus enriched in methane, favouring the formation of complex organic matter via radiation-induced polymerization of simple precursors. In contrast, production of complex organic matter is hindered in a nucleus possessing a low methane/water ration, with the complex organic matter that does form possessing more oxygen-containing species, such as alcohol, carbonyl and carboxylic acid functional groups, resulting from reactions with hydroxyl radicals formed by the radiolysis of the more abundant water. These insights into the properties of complex cometary organic matter should be of particular interest to both remote observation and space missions involving in situ analyses and sample return of cometary materials.

scholarly journals Use of optical absorption indices to assess seasonal variability of dissolved organic matter in Amazon floodplain lakes

2020 ◽  
Vol 17 (21) ◽  
pp. 5355-5364
Author(s):  
Maria Paula da Silva ◽  
Lino A. Sander de Carvalho ◽  
Evlyn Novo ◽  
Daniel S. F. Jorge ◽  
Claudio C. F. Barbosa
Keyword(s):  
Remote Sensing ◽  
Organic Matter ◽  
Optical Absorption ◽  
Dissolved Organic Matter ◽  
Seasonal Variability ◽  
Large Scale ◽  
Remote Sensing Data ◽  
Floodplain Lakes ◽  
Sentinel 2

Abstract. Given the importance of dissolved organic matter (DOM) in the carbon cycling of aquatic ecosystems, information on its seasonal variability is crucial. In this study we assess the use of optical absorption indices available in the literature based on in situ data to both characterize the seasonal variability of DOM in a highly complex environment and for application in large-scale studies using remote sensing data. The study area comprises four lakes located in the Mamirauá Sustainable Development Reserve (MSDR). Samples for the determination of colored dissolved organic matter (CDOM) and measurements of remote sensing reflectance (Rrs) were acquired in situ. The Rrs was used to simulate the response of the visible bands of the Sentinel-2 MultiSpectral Instrument (MSI), which was used in the proposed models. Differences between lakes were tested using the CDOM indices. The results highlight the role of the flood pulse in the DOM dynamics at the floodplain lakes. The validation results show that the use of the absorption coefficient of CDOM (aCDOM) as a proxy of the spectral slope between 275 and 295 nm (S275–295) during rising water is worthwhile, demonstrating its potential application to Sentinel-2 MSI imagery data for studying DOM dynamics on the large scale.

scholarly journals Use of absorption optical indices to assess seasonal variability of dissolved organic matter in amazon floodplain lakes

2019 ◽  
Author(s):  
Maria Paula da Silva ◽  
Lino A. Sander de Carvalho ◽  
Evlyn Novo ◽  
Daniel S. F. Jorge ◽  
Claudio C. F. Barbosa
Keyword(s):  
Remote Sensing ◽  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Seasonal Variability ◽  
Large Scale ◽  
River Bank ◽  
In Situ Data ◽  
Amazon Floodplain ◽  
Significant Difference

Abstract. Given the importance of DOM in the carbon cycling of aquatic ecosystems, information on its seasonal variability is crucial. This study assesses the use of available absorption optical indices based on in situ data to both characterize the seasonal variability of the DOM dynamics in a highly complex environment and their viability of being used for satellite remote sensing on large scale studies. The study area comprises four lakes located at the Mamirauá Sustainable Development Reserve (MSDR). Samples for the determination of coloured dissolved organic matter (CDOM) and remote sensing reflectance (Rrs) were acquired in situ. The Rrs was applied to simulate MSI visible bands and used in the proposed models. Differences between lakes were tested regarding CDOM indices. Significant difference in the average of aCDOM (440), aCDOM spectra and S275–295 were found between lakes located inside the flood forest and those near the river bank. The proposed model showed that aCDOM can be used as proxy of S275–295 during rising water with good validation results, demonstrating the potential of Sentinel/MSI imagery data in large scale studies on the dynamics of DOM.

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