scholarly journals Bottled aqua incognita: Microbiota assembly and dissolved organic matter diversity in natural mineral waters

2017 ◽  
Author(s):  
Celine C. Lesaulnier ◽  
Craig W. Herbold ◽  
Claus Pelikan ◽  
David Berry ◽  
Cédric Gérard ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Mineral Waters ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Natural Mineral ◽  
Operational Taxonomic Units ◽  
Abundant Otus ◽  
Low Concentrations ◽  
Carbon Molecules

ABSTRACTBackgroundNon-carbonated natural mineral waters contain microorganisms that regularly grow after bottling despite low concentrations of dissolved organic matter (DOM). Yet, the compositions of bottled water microbiota and organic substrates that fuel microbial activity, and how both change after bottling, are still largely unknown.ResultsWe performed a multifaceted analysis of microbiota and DOM diversity in twelve natural mineral waters from six European countries. 16S rRNA gene-based analyses showed that less than ten species-level operational taxonomic units (OTUs) dominated the bacterial communities in the water phase and associated with the bottle wall after a short phase of post-bottling growth. Members of the betaproteobacterial genera Curvibacter, Aquabacterium, and Polaromonas (Comamonadaceae) grew in most waters and represent ubiquitous, mesophilic, heterotrophic aerobes in bottled waters. Ultrahigh-resolution mass spectrometry of DOM in bottled waters and their corresponding source waters identified thousands of molecular formulae characteristic of mostly refractory, soil-derived DOM.ConclusionsThe bottle environment, including source water physicochemistry, selected for growth of a similar low-diversity microbiota across various bottled waters. Relative abundance changes of hundreds of multi-carbon molecules were related to growth of less than ten abundant OTUs. We thus speculate that individual bacteria cope with oligotrophic conditions by simultaneously consuming diverse DOM molecules.

scholarly journals Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters

Microbiome ◽  
2017 ◽  
Vol 5 (1) ◽  
Author(s):  
Celine C. Lesaulnier ◽  
Craig W. Herbold ◽  
Claus Pelikan ◽  
David Berry ◽  
Cédric Gérard ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Mineral Waters ◽  
Natural Mineral

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 as P source for biofilms in two contrasting low-order streams

2019 ◽  
Vol 193 (2) ◽  
pp. 131-142
Author(s):  
Verónica Díaz-Villanueva
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Deciduous Forest ◽  
Spatial Scales ◽  
Algal Species ◽  
Community Level ◽  
Nutrient Concentrations ◽  
Organic Substrates ◽  
One Year ◽  
Forest Streams

Forest streams receive large amounts of leaves whose leachates are an important source of dissolved organic matter (DOM), providing not only carbon but also organic nutrients to the microbial communities in streams. I carried out a field study to evaluate the effect of different DOM concentrations on the biofilm structure and functional traits in two similar forest streams belonging to the same catchment. I compared biofilm biomass and nutri- ent content throughout one year, algal species composition, and biofilm community-level physiological profiles in two streams with different DOM concentration and aromaticity. Dissolved nutrient concentrations were higher in the stream with higher DOM concentration, with a concomitant higher biofilm biomass, and there was also a temporal pattern, with higher values during the autumn. Phosphorus content in biofilms was also higher in the high DOM stream, coincidently with a higher capacity of the community to utilize organic P source (glucose-1-P) as a substrate. In contrast, the biofilms from the stream with lower DOM concentrations preferentially used N-organic substrates (amino acids and amines). These results reveal that the biofilms of forest streams make use of organic matter nutrients, so that streams with different DOM loads may differ in biofilm biomass due to changes in both bacterial and autotrophic biomass. In addition, biofilm dynamics may be related to forest phenology, as the highest OM input in this deciduous forest is represented by tree leaves, which supply DOM through leachates, and in particular, with P-rich leachates. In conclusion, different DOM concentrations in two nearby streams led to differences in the community-level physiological profile, as has been previously demonstrated at larger spatial scales in oceans, lakes and along larger rivers.

scholarly journals Diversity of Bacteria Growing in Natural Mineral Water after Bottling

2005 ◽  
Vol 71 (7) ◽  
pp. 3624-3632 ◽  
Author(s):  
Alexander Loy ◽  
Wolfgang Beisker ◽  
Harald Meier
Keyword(s):  
Bacterial Community ◽  
Bacterial Growth ◽  
Mineral Water ◽  
Bacterial Community Composition ◽  
Bacterial Flora ◽  
Significant Proportion ◽  
Mineral Waters ◽  
Rrna Gene ◽  
Natural Mineral ◽  
Natural Mineral Water

ABSTRACT Bacterial growth occurs in noncarbonated natural mineral waters a few days after filling and storage at room temperature, a phenomenon known for more than 40 years. Using the full-cycle rRNA approach, we monitored the development of the planktonic bacterial community in a noncarbonated natural mineral water after bottling. Seven 16S rRNA gene libraries, comprising 108 clones in total, were constructed from water samples taken at various days after bottling and from two different bottle sizes. Sequence analyses identified 11 operational taxonomic units (OTUs), all but one affiliated with the betaproteobacterial order Burkholderiales (6 OTUs) or the class Alphaproteobacteria (4 OTUs). Fluorescence in situ hybridization (FISH) was applied in combination with DAPI (4′,6′-diamidino-2-phenylindole) staining, viability staining, and microscopic counting to quantitatively monitor changes in bacterial community composition. A growth curve similar to that of a bacterium grown in a batch culture was recorded. In contrast to the current perception that Gammaproteobacteria are the most important bacterial components of natural mineral water in bottles, Betaproteobacteria dominated the growing bacterial community and accounted for 80 to 98% of all bacteria detected by FISH in the late-exponential and stationary-growth phases. Using previously published and newly designed genus-specific probes, members of the betaproteobacterial genera Hydrogenophaga, Aquabacterium, and Polaromonas were found to constitute a significant proportion of the bacterial flora (21 to 86% of all bacteria detected by FISH). For the first time, key genera responsible for bacterial growth in a natural mineral water were identified by applying molecular cultivation-independent techniques.

Organic matter content controls the N and P degradation process on biogeochemical interfaces: A micro-ecosystem scale study based on SoilChips-XPS-Zymography integrated technique in paddy soils

2020 ◽  
Author(s):  
Liang Wei
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Photoelectron Spectroscopy ◽  
Organic Matter Content ◽  
Degradation Process ◽  
Matter Content ◽  
Microbial Production ◽  
Paddy Soils ◽  
Rrna Gene ◽  
Degradation Processes

<p>The biogeochemical interfaces are hotspots for organic matter (OM) transformation. However, direct and continuouxiacis tracing of OM transformations and N and P degradation processes are lacking due to the heterogeneous and opaque nature of soil microenvironment. To investigate these processes, a new soil microarray technology (SoilChips) was developed and used. Homogeneous 2-mm-diameter SoilChips were constructed by depositing a dispersed paddy soils with high and low soil organic carbon (SOC) content. A horizon suspension on a patterned glass. Dissolved organic matter from the original soil was added on the SoilChips to mimic biogeochemical processes on interfaces. The chemical composition of biogeochemical interfaces were evaluated via X-ray photoelectron spectroscopy (XPS) and the two-dimensional distribution of enzyme activities in SoilChips were evaluated by zymography. Over 30 days, soil with high SOC content increases microbial nutrition (N and P) requirements than soil with low SOC evidenced by higher hotspots of β-1,4-N-acetaminophen glucosidase, and acid phosphomonoesterases and higher 16S rRNA gene copies. The degree of humification in dissolved organic matter (DOM) was higher and the bioavailability of DOM was poorer in soil with high SOC than soil with low SOC. The poorest bioavailability of DOM was detected at the end of incubation in soil with high SOC. Molecular modeling of OM composition showed that low SOC mainly facilitated the microbial production of glucans but high SOC mainly facilitated the microbial production of proteins. We demonstrated that SOC content or DOM availability for microorganisms modifies the specific OM molecular processing and N and P degradation processes, thereby providing a direct insight into biogeochemical transformation of OM at micro-scale.</p>

Acquiring reproducible fluorescence spectra of dissolved organic matter at very low concentrations

2009 ◽  
Vol 60 (6) ◽  
pp. 1385-1392 ◽  
Author(s):  
B. R. H. Peiris ◽  
H. Budman ◽  
C. Moresoli ◽  
R. L. Legge
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
High Concentration ◽  
Low Concentration ◽  
Low Concentrations ◽  
Fibre Optic Probe ◽  
On Line ◽  
Optic Probe ◽  
Membrane Treatment ◽  
Concentration Levels

A method that would allow for fast and reliable measurements of dissolved organic matter (DOM), both at low and high concentration levels would be a valuable tool for online monitoring of DOM. This could have applications in a variety of areas including membrane treatment systems for drinking water applications which is of interest to our group. In this study, the feasibility of using fluorescence spectroscopy for monitoring DOM at very low concentration levels was demonstrated with an emphasis on optimizing the instrument parameters necessary to obtain reproducible fluorescence signals. Signals were acquired using a cuvette or a fibre optic probe assembly, the latter which may have applications for on-line or in-line monitoring. The instrument parameters such as photomultiplier tube (PMT) voltage, scanning rate and slit width were studied in detail to find the optimum parameter settings required. The results showed that larger excitation and emission slit widths were preferred, over larger PMT voltage or lower scanning rates, to obtain reproducible and rapid measurements when measuring very low concentration levels of DOM. However, this approach should be implemented with caution to avoid any reduction of the signal resolution.

scholarly journals Composition and cycling of dissolved organic matter from tropical peatlands of coastal Sarawak, Borneo, revealed by fluorescence spectroscopy and PARAFAC analysis

2018 ◽  
Author(s):  
Yongli Zhou ◽  
Patrick Martin ◽  
Moritz Müller
Keyword(s):  
Organic Matter ◽  
Fluorescence Spectroscopy ◽  
Dissolved Organic Matter ◽  
Coastal Waters ◽  
Southeast Asian ◽  
Low Concentrations ◽  
Tropical Peatlands ◽  
Shelf Seas ◽  
High Concentrations ◽  
High Degree

Abstract. Southeast Asian peatlands supply ~ 10 % of the global flux of dissolved organic carbon (DOC) from land to the ocean, but the biogeochemical cycling of this peat-derived DOC in coastal environments is still poorly understood. Here, we use fluorescence spectroscopy and parallel factor (PARAFAC) analysis to distinguish different fractions of dissolved organic matter (DOM) in peat-draining rivers, estuaries, and coastal waters of Sarawak, Borneo. The terrigenous fractions showed high concentrations at freshwater stations within the rivers, and conservative mixing with seawater across the estuaries. The autochthonous DOM fraction, in contrast, showed low concentrations throughout our study area at all salinities. The DOM pool was also characterized by a high degree of humification in all rivers and estuaries up to salinity 25. These results indicate a predominantly terrestrial origin of the riverine DOM pool. Only at salinities > 25 did we observe an increase in the proportion of autochthonous relative to terrestrial DOM. Natural sunlight exposure experiments with river water and seawater showed high photolability of the terrigenous DOM fractions, suggesting that photodegradation may account for the observed changes in DOM composition in coastal waters. Nevertheless, we estimate based on our fluorescence data that at least 20 %–25 % of the DOC at even our most marine stations (salinity > 31) was terrestrial in origin, indicating that peatlands likely play an important role in the carbon biogeochemistry of Southeast Asian shelf seas.

scholarly journals Combining Culture-Dependent and -Independent Methodologies for Estimation of Richness of Estuarine Bacterioplankton Consuming Riverine Dissolved Organic Matter

2003 ◽  
Vol 69 (6) ◽  
pp. 3607-3616 ◽  
Author(s):  
Veljo Kisand ◽  
Johan Wikner
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Experimental System ◽  
Community Diversity ◽  
Rrna Gene ◽  
Solid Media ◽  
Gradient Gel Electrophoresis ◽  
Culture Dependent

ABSTRACT Three different methods for analyzing natural microbial community diversity were combined to maximize an estimate of the richness of bacterioplankton catabolizing riverine dissolved organic matter (RDOM). We also evaluated the ability of culture-dependent quantitative DNA-DNA hybridization, a 16S rRNA gene clone library, and denaturing gradient gel electrophoresis (DGGE) to detect bacterial taxa in the same sample. Forty-two different cultivatable strains were isolated from rich and poor solid media. In addition, 50 unique clones were obtained by cloning of the bacterial 16S rDNA gene amplified by PCR from the community DNA into an Escherichia coli vector. Twenty-three unique bands were sequenced from 12 DGGE profiles, excluding a composite fuzzy band of the Cytophaga-Flavobacterium group. The different methods gave similar distributions of taxa at the genus level and higher. However, the match at the species level among the methods was poor, and only one species was identified by all three methods. Consequently, all three methods identified unique subsets of bacterial species, amounting to a total richness of 97 operational taxonomic units in the experimental system. The confidence in the results was, however, dependent on the current precision of the phylogenetic determination and definition of the species. Bacterial consumers of RDOM in the studied estuary were primarily both cultivatable and uncultivable taxa of the Cytophaga-Flavobacterium group, a concordant result among the methods applied. Culture-independent methods also suggested several not-yet-cultivated β-proteobacteria to be RDOM consumers.

scholarly journals Modeling the action of anaerobic biofilm

2021 ◽  
pp. 52-58
Author(s):  
V. L. Poliakov
Keyword(s):  
Fatty Acids ◽  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Volatile Fatty Acids ◽  
Analytic Solution ◽  
Mathematical Problem ◽  
Approximate Analytic Solution ◽  
Organic Substrates ◽  
Vital Activity ◽  
Stage Process

A mathematical problem of the action of a representative biofilm in the absence of oxygen is formulated. The anaerobic process of decomposition of a dissolved organic matter is considered as a two-stage process, proceeding due to the vital activity of two groups of microorganisms. An approximate analytic solution allowing one to calculate the concentration and consumption of primary and secondary organic substrates with minimal errors has been obtained. On test examples, their rates of transfer through the biofilm surface are determined, and the possibility of the movement of volatile fatty acids in both directions is discussed.

scholarly journals Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites

2019 ◽  
Vol 95 (9) ◽  
Author(s):  
Elisabeth M Happel ◽  
Trine Markussen ◽  
Jonna E Teikari ◽  
Vimala Huchaiah ◽  
Johannes Alneberg ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Baltic Sea ◽  
Community Composition ◽  
N Cycling ◽  
Rrna Gene ◽  
The Baltic Sea ◽  
Microbial Composition ◽  
Catchment Areas ◽  
The Baltic

ABSTRACT Heterotrophic bacteria are important drivers of nitrogen (N) cycling and the processing of dissolved organic matter (DOM). Projected increases in precipitation will potentially cause increased loads of riverine DOM to the Baltic Sea and likely affect the composition and function of bacterioplankton communities. To investigate this, the effects of riverine DOM from two different catchment areas (agricultural and forest) on natural bacterioplankton assemblages from two contrasting sites in the Baltic Sea were examined. Two microcosm experiments were carried out, where the community composition (16S rRNA gene sequencing), the composition of a suite of N-cycling genes (metagenomics) and the abundance and transcription of ammonia monooxygenase (amoA) genes involved in nitrification (quantitative PCR) were investigated. The river water treatments evoked a significant response in bacterial growth, but the effects on overall community composition and the representation of N-cycling genes were limited. Instead, treatment effects were reflected in the prevalence of specific taxonomic families, specific N-related functions and in the transcription of amoA genes. The study suggests that bacterioplankton responses to changes in the DOM pool are constrained to part of the bacterial community, whereas most taxa remain relatively unaffected.

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