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Abstract

Diverse prokaryotic communities consume and transform a broad suite of molecules in the dissolved organic matter (DOM) pool, which controls major biogeochemical cycles. Despite methodological advancements that provide increasingly more detailed information on the diversity of both prokaryotic communities and DOM components, understanding how these two component parts are structured to influence ecosystem functioning remains a major challenge in microbial ecology. Using empirical data collected along a gradient of productivity in the Labrador Sea, we characterized relationships among DOM compounds, metabolic processing, and prokaryotic diversity by structuring prokaryotic communities using spatial abundance distribution (SpAD) modeling. We identified strong associations of different SpAD taxonomic groups with specific organic substrates as well as with metabolic rates. Amplicon sequence variants (ASVs) with more cosmopolitan distributions (i.e. normal‐like) such as Bacteroidia were related to fresher DOM substrates such as free and combined amino acids whereas rare ASVs (i.e. logistic) like δ‐proteobacteria were associated with complex forms of organic matter. In terms of ecosystem function, rates of respiration and production were most strongly predicted by the abundance of certain SpAD taxonomic groups. Given the importance and complexity of linking environmental conditions, prokaryotic community structure, and ecosystem function, we propose a framework to bridge the gap between prokaryotic diversity, microbial ecology, and biogeochemistry among methods and across scales. Our work suggests that SpAD modeling can be used as an intermediate step to link prokaryotic community structure to both finer DOM details and larger ecosystem scale processes.

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... One of the major differences we observed between the surface versus the deeper meso-and bathypelagic treatments was the high read abundance of Pelagibacter, a taxa that represents about half of all living microbes in the surface ocean (49). However, their total abundance in the surface microcosms remained rather constant throughout the incubations, suggesting that they were not particularly active even when more labile substrates were available during the first 2 weeks of the incubation, which resembled bloom conditions at the study site (50). This apparent inactivity of Pelagibacter was also observed in other studies (44,50) and can also explain the slight difference in the relative abundance of the rare biosphere between the two deeper treatments (Fig. 4D) as Pelagibacter accounted for about 10% of the bathypelagic community near the end of the incubation. ...
... However, their total abundance in the surface microcosms remained rather constant throughout the incubations, suggesting that they were not particularly active even when more labile substrates were available during the first 2 weeks of the incubation, which resembled bloom conditions at the study site (50). This apparent inactivity of Pelagibacter was also observed in other studies (44,50) and can also explain the slight difference in the relative abundance of the rare biosphere between the two deeper treatments (Fig. 4D) as Pelagibacter accounted for about 10% of the bathypelagic community near the end of the incubation. A more responsive taxa in the surface treatment was Polaribacter whose read abundance followed total cell counts. ...
... To avoid contamination, 1-liter samples were collected from each microcosm into an acidwashed, preconditioned glass bottle and then subsampled using a nano-pure water-rinsed, preconditioned 60-ml glass syringe with silicone tubing for DOM and prokaryotic characterization. Measurements were chosen to describe specific components of DOM-microbe interactions (50). Although DOM and DOC are often used interchangeably, we used DOC when specifically referring to carbon and to DOM otherwise. ...
Article
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... Previous studies have found chemical differences (such as the availability and quality of nutrients) that determine the presence or absence of certain bacterial species Zhang et al., 2021a). Furthermore, environmental filtering is a key determinant of microbial community assembly, and many studies have shown that pH, organic matters, and salinity can influence the assembly and biogeographic pattern of bacterial community processes in various environments LaBrie et al., 2021;Yang et al., 2016). This study found that the heavy metals Zn, Cd, Hg, Pb, and As had significant negative regulation on the core and occasional taxa in the plastisphere, which may be due to the plastic adsorption of heavy metals driving bacterial communities towards increased taxonomic and phylogenetic sorting. ...
Article
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... In the future, the importance of stochastic biogeographic processes in the assembly of early subsurface microbial communities could be further investigated by applying neutral and nullmodel approaches (Stegen et al., 2013;LaBrie et al., 2020), which might be more adapted to detecting the influence of drift in particular. In addition, part of the unexplained variation detected in our data is probably linked to biotic interactions with organisms not covered in this study (Gralka et al., 2020;Tobias-Hünefeldt et al., 2020), and may thus be further elucidated with metabarcoding data being generated for metazoans and protists in the scope of this project. ...
Thesis
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... DOM exported to the mesopelagic via physical mixing contains a continuous spectrum of compounds with varying lability and corresponding myriad responses from bacterial taxa with different nutrition-acquisition strategies and effective niches (Fuhrman and Hagström, 2008;LaBrie et al., 2020;Liu et al., 2020a). Bacteria characterized as copiotrophs such as members of the Rhodobacterales and Rhodospirillales clades are often associated with elevated primary production Buchan et al., 2014;Wilson et al., 2017). ...
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Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016–2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades, Acidimicrobiales, and Flavobacteria, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.
... The different shapes can be interpreted as ecological traits because the abundance distribution of a given taxon will be the result of the combination of its physiological capacities, environmental tolerances or ability to persist under unfavourable conditions, but also of the external factors controlling its abundance. This approach has been previously used to explore the mechanisms behind the ubiquity or rarity of taxa within aquatic prokaryotic or picoeukaryotic communities (Niño-García et al., 2016;Mangot et al., 2018;Ruiz-Gonz alez et al., 2019;LaBrie et al., 2021), but to our knowledge, this is the first time that it is restrictively applied to a functional group. ...
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The aerobic anoxygenic phototrophic (AAP) bacteria are common in most marine environments but their global diversity and biogeography remain poorly characterized. Here, we analyzed AAP communities across 113 globally-distributed surface ocean stations sampled during the Malaspina Expedition in the tropical and subtropical ocean. By means of amplicon sequencing of the pufM gene, a genetic marker for this functional group, we show that AAP communities along the surface ocean were mainly composed of members of the Halieaceae (Gammaproteobacteria), which were adapted to a large range of environmental conditions, and of different clades of the Alphaproteobacteria, which seemed to dominate under particular circumstances, such as in the oligotrophic gyres. AAP taxa were spatially structured within each of the studied oceans, with communities from adjacent stations sharing more taxonomic similarities. AAP communities were composed of a large pool of rare members and several habitat specialists. When compared to the surface ocean prokaryotic and picoeukaryotic communities, it appears that AAP communities display an idiosyncratic global biogeographical pattern, dominated by selection processes and less influenced by dispersal limitation. Our study contributes to the understanding of how AAP communities are distributed in the horizontal dimension and the mechanisms underlying their distribution across the global surface ocean.
... In the future, the importance of stochastic biogeographic processes in the assembly of early subsurface microbial communities could be further investigated by applying neutral and null-model approaches (Stegen et al., 2013;LaBrie et al., 2021), which might be more adapted to detecting the influence of drift in particular. In addition, part of the unexplained variation detected in our data is probably linked to biotic interactions with organisms not covered in this study (Gralka et al., 2020;Tobias-Hünefeldt et al., 2021), and may thus be further elucidated with metabarcoding data being generated for metazoans and protists in the scope of this project. ...
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Seafloor sediments cover the majority of planet Earth and microorganisms inhabiting these environments play a central role in marine biogeochemical cycles. Yet, description of the biogeography and distribution of sedimentary microbial life is still too sparse to evaluate the relative contribution of processes driving this distribution, such as the levels of drift, connectivity, and specialization. To address this question, we analyzed 210 archaeal and bacterial metabarcoding libraries from a standardized and horizon-resolved collection of sediment samples from 18 stations along a longitudinal gradient from the eastern Mediterranean to the western Atlantic. Overall, we found that biogeographic patterns depended on the scale considered: while at local scale the selective influence of contemporary environmental conditions appeared strongest, the heritage of historic processes through dispersal limitation and drift became more apparent at regional scale, and ended up superseding contemporary influences at inter-regional scale. When looking at environmental factors, the structure of microbial communities was correlated primarily with water depth, with a clear transition between 800 and 1,200 meters below sea level. Oceanic basin, water temperature, and sediment depth were other important explanatory parameters of community structure. Finally, we propose increasing dispersal limitation and ecological drift with sediment depth as a probable factor for the enhanced divergence of deeper horizons communities.
... Environmental filtering is a key determinant of microbial community assembly and many studies have shown that pH, organic matters, and salinity can influence bacterial community assembly processes in various environments (Jiao and Lu, 2020a;LaBrie et al., 2021;Yang et al., 2016). Environmental factors such as TN and TP are the main indicators for evaluating the degree of lake eutrophication (Du et al., 2019;Lin et al., 2020). ...
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Eutrophication of freshwater lakes is an important cause of global water pollution. In this study, the composition and biogeographic distribution of both abundant and rare sedimentary bacterial taxa and their relationship with nutrients were assessed in Erhai Lake, a subtropical plateau lake. Proteobacteria (48.3%) and Nitrospirae (11.7%) dominated the composition of abundant taxa, while the rare taxa were dominated by Proteobacteria (25.8%) and Chloroflexi (14.1%). The abundant bacterial taxa had strong energy metabolism, whereas the rare bacterial taxa had strong xenobiotics biodegradation and metabolism. These results indicated different compositions and functions existed between abundant and rare taxa. Total nitrogen (TN) was the most influential factor shaping the biogeographic patterns of both abundant and rare taxa. Phosphorus was not the deterministic factor, although nitrogen and phosphorus were the main contributors to eutrophication. Total organic carbon and pH also contributed to the biogeographic patterns of both abundant and rare taxa. In the eutrophic plateau lake sediments, abundant taxa, rather than rare taxa, played a dominant role in maintaining the community structure and ecological function of the bacterial community. The TN gradient was an important factor that affected the biogeographic distribution and assembly processes of abundant taxa. This study sheds light on the role of TN in shaping the biogeographic distribution and assembly processes of abundant taxa in eutrophic lakes.
... Furthermore, the flux of particles reaching the 76 bathypelagic is variable over time [2,18,19], and thus bathypelagic communities must 77 have adapted to these intermittent carbon inputs. 78 Particle-attached and free-living communities in the bathypelagic differ in dominant 79 phyla and/or classes [20], suggesting that these lifestyles have been strongly conserved 80 through the evolutionary history of deep-sea prokaryotes. One possible driver of this 81 evolution is the nature of the organic carbon sources available to these two communities. ...
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Marine dissolved organic matter (DOM) is one of the largest reservoirs of reduced carbon on Earth. In the dark ocean (4200 m), most of this carbon is refractory DOM. This refractory DOM, largely produced during microbial mineralization of organic matter, includes humic-like substances generated in situ and detectable by fluorescence spectroscopy. Here we show two ubiquitous humic-like fluorophores with turnover times of 435 ± 41 and 610 ± 55 years, which persist significantly longer than the B350 years that the dark global ocean takes to renew. In parallel, decay of a tyrosine-like fluorophore with a turnover time of 379 ± 103 years is also detected. We propose the use of DOM fluorescence to study the cycling of resistant DOM that is preserved at centennial timescales and could represent a mechanism of carbon sequestration (humic-like fraction) and the decaying DOM injected into the dark global ocean, where it decreases at centennial timescales (tyrosine-like fraction).
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Soil microbial communities perform many important processes, including nutrient cycling, plant-microorganism interactions, and degradation of xenobiotics. The study of microbial communities, however, has been limited by cultural methods, which may greatly underestimate diversity. The advent of nucleic acids technologies allows microbial communities to be quantified and classified without the limitations of cultivation. Fluorescent in situ hybridization (FISH) and other tools of molecular ecology are now being used to investigate community structure and diversity of soils, aquifers, and other natural habitats. Based on these studies, soil microbial communities are diverse and appear to respond to anthropogenic inputs, such as fertilizer, manure, and pollutants, as well as the more well-known constraints imposed by temperature and moisture. Yet most nucleic-acids-based technologies are unable to directly link phylogeny with processes in a manner similar to cultivation-based approaches, restricting the conclusions that can be drawn from the large data sets they generate. Recently, the combination of FISH with microautoradiography (FISH-MAR) allows cells active in processes to be quantified and simultaneously classified phylogenetically. In this review, we discuss how FISH-MAR can be used to quantify the specific microbial phylotype(s) responsible for a microbially catalyzed process. Examples of the use of FISH and FISH-MAR in soils and sediments are described. The capabilities and limitations of these techniques for linking microbial community structure and function are discussed.
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There is as much carbon in dissolved organic material in the oceans as there is CO2 in the atmosphere, but the role of dissolved organic carbon (DOC) in the global carbon cycle is poorly understood. DOC in the deep ocean has long been considered to be uniformly distributed and hence largely refractory to biological decay. But the turnover of DOC, and therefore its contribution to the carbon cycle, has been evident from radiocarbon dating studies. Here we report the results of a global survey of deep-ocean DOC concentrations, including the region of deep-water formation in the North Atlantic Ocean, the Circumpolar Current of the Southern Ocean, and the Indian and Pacific oceans. DOC concentrations decreased by 14 micromolar from the northern North Atlantic Ocean to the northern North Pacific Ocean, representing a 29% reduction in concentration. We evaluate the spatial patterns in terms of source/sink processes. Inputs of DOC to the deep ocean are identifiable in the mid-latitudes of the Southern Hemisphere, but the mechanisms have not been identified with certainty.
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Marine dissolved organic carbon (DOC) exhibits a spectrum of reactivity, from very fast turnover of the most bioavailable forms in the surface ocean to long-lived materials circulating within the ocean abyss. These disparate reactivities group DOC by fractions with distinctive functions in the cycling of carbon, ranging from support of the microbial loop to involvement in the biological pump to a hypothesized major source/sink of atmospheric CO(2) driving paleoclimate variability. Here, the major fractions constituting the global ocean's recalcitrant DOC pool are quantitatively and qualitatively characterized with reference to their roles in carbon biogeochemistry. A nomenclature for the fractions is proposed based on those roles. Expected final online publication date for the Annual Review of Marine Science Volume 5 is December 05, 2012. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.
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1] We measured the absorption properties of phytoplankton, nonalgal particles (NAP), and colored dissolved organic matter (CDOM) at about 350 stations in various coastal waters around Europe including the English Channel, Adriatic Sea, Baltic Sea, Mediterranean Sea, and North Sea. For comparison, we also collected data in the open ocean waters of North Atlantic. The exponential slope of the CDOM absorption spectrum varied within a narrow range around 0.0176 nm À1 (SD = 0.0020 nm À1). When data from all the regions were considered altogether, the relationship between phytoplankton absorption and chlorophyll concentration was generally similar to the one previously established for open oceanic waters. Our coastal data, however, show that significant departures from the general trend may occur due to peculiar pigment composition and cell size. In some coastal areas, high phaeopigment concentrations gave rise to especially high blue-to-red ratio of phytoplankton absorption. The NAP absorption covaried with the particle dry weight. Most absorption spectra of these particles were well described by an exponential function with a slope averaging 0.0123 nm À1 (SD = 0.0013 nm À1). In some highly turbid waters, the spectra exhibited a signature possibly associated with iron oxides. In the Baltic Sea, NAP absorption systematically showed lower values at wavelengths shorter than 440 nm than predicted from the fitted exponential function. Overall, the variability in the absorption properties of European coastal waters showed some consistent patterns despite the high diversity of the examined waters. Distinct features were identified in the phytoplankton and NAP components. An absorption budget is presented and parameterizations are proposed., Variations in the light absorption coefficients of phytoplankton, nonalgal particles, and dissolved organic matter in coastal waters around Europe, J. Geophys. Res., 108(C7), 3211, doi:10.1029/2001JC000882, 2003.
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Phytoplankton blooms characterize temperate ocean margin zones in spring. We investigated the bacterioplankton response to a diatom bloom in the North Sea and observed a dynamic succession of populations at genus-level resolution. Taxonomically distinct expressions of carbohydrate-active enzymes (transporters; in particular, TonB-dependent transporters) and phosphate acquisition strategies were found, indicating that distinct populations of Bacteroidetes, Gammaproteobacteria, and Alphaproteobacteria are specialized for successive decomposition of algal-derived organic matter. Our results suggest that algal substrate availability provided a series of ecological niches in which specialized populations could bloom. This reveals how planktonic species, despite their seemingly homogeneous habitat, can evade extinction by direct competition.
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Recently developed techniques for estimating bacterial biomass and productivity indicate that bacterial biomass in the sea is related to phytoplankton concentration and that bacteria utilise 10 to 50 % of carbon fixed by photosynthesis. Evidence is presented to suggest that numbers of free bacteria are controlled by nanoplankton~c heterotrophic flagellates which are ubiquitous in the marine water column. The flagellates in turn are preyed upon by microzooplankton. Heterotrophic flagellates and microzooplankton cover the same size range as the phytoplankton, thus providing the means for returning some energy from the 'microbial loop' to the conventional planktonic food chain.
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Modern data acquisition based on high-throughput technology is often facing the problem of missing data. Algorithms commonly used in the analysis of such large-scale data often depend on a complete set. Missing value imputation offers a solution to this problem. However, the majority of available imputation methods are restricted to one type of variable only: continuous or categorical. For mixed-type data, the different types are usually handled separately. Therefore, these methods ignore possible relations between variable types. We propose a non-parametric method which can cope with different types of variables simultaneously. We compare several state of the art methods for the imputation of missing values. We propose and evaluate an iterative imputation method (missForest) based on a random forest. By averaging over many unpruned classification or regression trees, random forest intrinsically constitutes a multiple imputation scheme. Using the built-in out-of-bag error estimates of random forest, we are able to estimate the imputation error without the need of a test set. Evaluation is performed on multiple datasets coming from a diverse selection of biological fields with artificially introduced missing values ranging from 10% to 30%. We show that missForest can successfully handle missing values, particularly in datasets including different types of variables. In our comparative study, missForest outperforms other methods of imputation especially in data settings where complex interactions and non-linear relations are suspected. The out-of-bag imputation error estimates of missForest prove to be adequate in all settings. Additionally, missForest exhibits attractive computational efficiency and can cope with high-dimensional data. The package missForest is freely available from http://stat.ethz.ch/CRAN/. stekhoven@stat.math.ethz.ch; buhlmann@stat.math.ethz.ch
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An understanding of the distribution of colored dissolved organic matter (CDOM) in the oceans and its role in the global carbon cycle requires a better knowledge of the colored materials produced and consumed by marine phytoplankton and bacteria. In this work, we examined the net uptake and release of CDOM by a natural bacterial community growing on DOM derived from four phytoplankton species cultured under axenic conditions. Fluorescent humic-like substances exuded by phytoplankton (excitation/emission [Ex/Em] wavelength, 310 nm/392 nm; Coble's peak M) were utilized by bacteria in different proportions depending on the phytoplankton species of origin. Furthermore, bacteria produced humic-like substances that fluoresce at an Ex/Em wavelength of 340 nm/440 nm (Coble's peak C). Differences were also observed in the Ex/Em wavelengths of the protein-like materials (Coble's peak T) produced by phytoplankton and bacteria. The induced fluorescent emission of CDOM produced by prokaryotes was an order of magnitude higher than that of CDOM produced by eukaryotes. We have also examined the final compositions of the bacterial communities growing on the exudates, which differed markedly depending on the phytoplankton species of origin. Alteromonas and Roseobacter were dominant during all the incubations on Chaetoceros sp. and Prorocentrum minimum exudates, respectively. Alteromonas was the dominant group growing on Skeletonema costatum exudates during the exponential growth phase, but it was replaced by Roseobacter afterwards. On Micromonas pusilla exudates, Roseobacter was replaced by Bacteroidetes after the exponential growth phase. Our work shows that fluorescence excitation-emission matrices of CDOM can be a helpful tool for the identification of microbial sources of DOM in the marine environment, but further studies are necessary to explore the association of particular bacterial groups with specific fluorophores.
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Dormancy is a bet-hedging strategy used by a variety of organisms to overcome unfavorable environmental conditions. By entering a reversible state of low metabolic activity, dormant individuals become members of a seed bank, which can determine community dynamics in future generations. Although microbiologists have documented dormancy in both clinical and natural settings, the importance of seed banks for the diversity and functioning of microbial communities remains untested. Here, we develop a theoretical model demonstrating that microbial communities are structured by environmental cues that trigger dormancy. A molecular survey of lake ecosystems revealed that dormancy plays a more important role in shaping bacterial communities than eukaryotic microbial communities. The proportion of dormant bacteria was relatively low in productive ecosystems but accounted for up to 40% of taxon richness in nutrient-poor systems. Our simulations and empirical data suggest that regional environmental cues and dormancy synchronize the composition of active communities across the landscape while decoupling active microbes from the total community at local scales. Furthermore, we observed that rare bacterial taxa were disproportionately active relative to common bacterial taxa, suggesting that microbial rank-abundance curves are more dynamic than previously considered. We propose that repeated transitions to and from the seed bank may help maintain the high levels of microbial biodiversity that are observed in nearly all ecosystems.
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We used a method that combines microautoradiography with hybridization of fluorescent rRNA-targeted oligonucleotide probes to whole cells (MICRO-FISH) to test the hypothesis that the relative contributions of various phylogenetic groups to the utilization of dissolved organic matter (DOM) depend solely on their relative abundance in the bacterial community. We found that utilization of even simple low-molecular-weight DOM components by bacteria differed across the major phylogenetic groups and often did not correlate with the relative abundance of these bacterial groups in estuarine and coastal environments. The Cytophaga-Flavobacter cluster was overrepresented in the portion of the assemblage consuming chitin,N-acetylglucosamine, and protein but was generally underrepresented in the assemblage consuming amino acids. The amino acid-consuming assemblage was usually dominated by the α subclass of the class Proteobacteria, although the representation of α-proteobacteria in the protein-consuming assemblages was about that expected from their relative abundance in the entire bacterial community. In our experiments, no phylogenetic group dominated the consumption of all DOM, suggesting that the participation of a diverse assemblage of bacteria is essential for the complete degradation of complex DOM in the oceans. These results also suggest that the role of aerobic heterotrophic bacteria in carbon cycling would be more accurately described by using three groups instead of the single bacterial compartment currently used in biogeochemical models.
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Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA‐defined Operational Taxonomic Units, OTUs) across 108 globally‐distributed surface ocean stations. We grouped taxa based on their SpAD shape (‘normal‐like’‐ abundant and ubiquitous; ‘logistic’‐ globally rare, present in few sites; and ‘bimodal’‐ abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan ‘normal‐like’ OTUs, yet there was a gradual shift towards assemblages dominated by ‘logistic’ taxa in specific areas with productivity and temperature differing most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and suspended particles), the SpAD of many OTUs changed towards fewer ‘normal‐like’ shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members. This article is protected by copyright. All rights reserved.
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In environmental engineering and science, fluorescent excitation-emission matrix (EEM) has increasingly been utilized to characterize chromophoric dissolved organic matter (CDOM). This study aims to delineate EEM data processing, including calculation of total fluorescence (TF) which is an emerging water quality parameter often used as a surrogate for micropollutant removal by advanced water treatment processes. In addition, sample handling procedures such as storage, use of preservatives, and oxidant quenching agents were evaluated. In this study, three antimicrobial preservatives were tested: sodium azide, sodium omadine, and thymol. All the tested preservatives altered optical properties of samples, and were therefore not suitable for the preservation of EEM samples. Without preservative, storage of samples at 4 °C maintained TF within 7.5% of its original value for 21 days, while TF of samples stored at the room temperature more drastically changed (up to 15%). The impacts of three oxidant quenching agents including ascorbic acid, sodium bisulfite, and sodium thiosulfate on EEM were also tested. Among the quenching agents, sodium bisulfite was found to be suitable since it little influenced optical properties of samples while the other two were not favorable due to interference. We also scrutinized the use of TF as surrogate to monitor micropollutant rejection by nanofiltration membrane.
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The reason behind the millennial stability of marine dissolved organic matter (DOM) is subject of controversial discussion. It may be derived by either the occurrence of mainly stable chemical structures or concentrations of individual DOM molecules too low for efficient microbial growth. One of the major challenges in solving this enigma is that, to date, full structural elucidation of DOM remains impossible. Ultrahigh-resolution mass spectrometry can resolve the composition of DOM on a molecular formula level, but the molecular diversity of the isomers behind each formula is unknown. The objective of our study was to fill this gap of knowledge. Molecular fragmentation experiments were performed via Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) on single substances and molecular formulae isolated from deep-sea DOM. We estimated carboxyl (COOH) content with help of two novel measures, one derived from molecular formula information alone and one from fragment ion intensities. For the carboxyl content of single substances, they were poor predictors and fragment ion intensities were highly sensitive to structural properties. For natural DOM, on the contrary, both parameters were highly significantly correlated, despite obvious structural differences between the molecular formulae considered in this study. By using a model approach based on the central limit theorem, we were able to show that the observed fragment ion intensities of DOM may be explained by intrinsic averaging. These results are clear experimental evidence that many isomers exist per molecular formula. Model calculations showed that the observable molecular properties of DOM apparently emerged as averages of multiple isomers according to the central limit theorem. Structural differences between isomers that would reduce the accuracy of our measures for carboxyl content lost their effect due to averaging. Our model calculations based on the central limit theorem indicated that there are at least 100,000 different compounds in DOM each present in seawater at picomolar concentrations.
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Aquatic bacterial communities harbour thousands of coexisting taxa. To meet the challenge of discriminating between a ‘core’ and a sporadically occurring ‘random’ component of these communities, we explored the spatial abundance distribution of individual bacterioplankton taxa across 198 boreal lakes and their associated fluvial networks (188 rivers). We found that all taxa could be grouped into four distinct categories based on model statistical distributions (normal like, bimodal, logistic and lognormal). The distribution patterns across lakes and their associated river networks showed that lake communities are composed of a core of taxa whose distribution appears to be linked to in-lake environmental sorting (normal-like and bimodal categories), and a large fraction of mostly rare bacteria (94% of all taxa) whose presence appears to be largely random and linked to downstream transport in aquatic networks (logistic and lognormal categories). These rare taxa are thus likely to reflect species sorting at upstream locations, providing a perspective of the conditions prevailing in entire aquatic networks rather than only in lakes.
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SAR11 is a group of small, carbon-oxidizing cells that reach a global estimated population size of 2.4 × 1028 cells—approximately 25% of all plankton. They are found throughout the oceans but reach their largest numbers in stratified, oligotrophic gyres, which are an expanding habitat in the warming oceans. SAR11 likely had a Precambrian origin and, over geological time, evolved into the niche of harvesting labile, low-molecular-weight dissolved organic matter (DOM). SAR11 cells are minimal in size and complexity, a phenomenon known as streamlining that is thought to benefit them by lowering the material costs of replication and maximizing transport functions that are essential to competition at ultralow nutrient concentrations. One of the surprises in SAR11 metabolism is their ability to both oxidize and produce a variety of volatile organic compounds that can diffuse into the atmosphere. SAR11 cells divide slowly and lack many forms of regulation commonly used by bacterial cells to adjust to changing environmental conditions. As a result of genome reduction, they require an unusual range of nutrients, which leads to complex biochemical interactions with other plankton. The study of SAR11 is providing insight into the biogeochemistry of labile DOM and is affecting microbiology beyond marine science by providing a model for understanding the evolution and function of streamlined cells. Expected final online publication date for the Annual Review of Marine Science Volume 9 is January 03, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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The concentration of chlorophyll in laboratory grown cultures of marine phytoplankton and in oceanic samples has been determined both by measurement of fluorescence and by measurement of light absorption. The lower limit for detection of chlorophyll by fluorescence with the instrumentation described is about 0·01 μg chlorophyll a, which is about 5% that required for a spectro-photometric determination. Through choice of appropriate filters, the amount of fluorescence reflects either the chlorophyll a concentration or the sum of chlorophylls a and c. By measurement of fluorescence before and after acidification, the ratio of chlorophyll to phaeophytin can be readily determined. Dilute HCl is superior to oxalic acid for acidification of pigment extracts. As the fluorometric determination of chlorophyll and phaeophytin is fast, reliable and sensitive, it will be very useful in field studies of productivity.
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Acid hydrolysis-induced racemization compromises accurate determination of enantiomeric amino acid compositions. In the present study, the extent of amino acid racemization during a vapor (6 M HCl, 32.5 min, 150°C) and liquid-phase hydrolysis (6 M HCl, 20 h, 110°C) was assessed, and the influence on the accuracy of enantiomer measurements was investigated. The extent of hydrolysis-induced racemization was controlled by the molecular structure of the amino acid polymer and hydrolysis conditions. Vapor-phase hydrolysis showed significantly higher racemization compared to liquid-phase hydrolysis. Without correction, hydrolysis-induced racemization resulted in overestimation of D-enantiomers and could lead to erroneous conclusions about the occurrence of D-enantiomers in natural samples. The range of racemization was determined with proteins and free amino acids, and an averaged racemization value is proposed to account for enantiomer exchange during hydrolysis. In addition, a microwave-assisted vapor-phase hydrolysis is described that allows preparation of 40 samples in about 3 h with very low blanks. © 2005, by the American Society of Limnology and Oceanography, Inc.
Chapter
Introduction Major Groups of Prokaryotes in Seawater “Classically” Culturable Bacteria “Sea Water” Culturable Bacteria Not-Yet-Cultured Bacteria Marine Archaea Bacterioplankton Diversity Community Structure: Description and Factors Temporal Variation (Days to Seasonal) Spatial Variation Summary References
Article
Dissolved organic substances (carbohydrates, organic nitrogen, free amino acids) were measured in the German Bight (North Sea) in June, 1981. During and before this survey, sea foam was observed in the east Frisian coastal water and it accumulated on the nearby beaches to an unusually high extent. In this coastal water area, a large Phaeocystis pouchetii Lagerheim bloom and very high concentrations of dissolved organic matter were found. The above dissolved organic substances were all positively correlated to a highly significant degree with P. pouchetii cell numbers in the bloom area. An influence of salinity (or river water) on this correlation could be excluded. Thus, exudation or decomposition products of P. pouchetii were most likely the cause of the unusually high concentrations of dissolved organic matter in the bloom area off the east Frisian coast, where P. pouchetii blooms have been reported for many years. Ammonia concentrations were very low in the P. pouchetii bloom area; this and the accumulation of dissolved organic substances might lead to speculation that decomposition of dissolved organic matter by bacteria could have been reduced due to antibiotic activity of P. pouchetii.
Article
A systematic survey of the protein-like fluorescence intensities was conducted at 11 stations along the 137°E transect from bay to oceanic areas in the northwestern Pacific using three-dimensional excitation emission matrix (3DEEM) spectroscopy and the concentrations of aromatic amino acids obtained by high-performance liquid chromatography (HPLC) in dissolved organic matter (DOM). The 3DEEM patterns of tyrosine-like and tryptophan-like peaks in protein-like fluorophores were variable across different marine environments. The tyrosine-like peak was observed at all stations and depths, while the tryptophan-like peak was only distinguishable as a clear peak in bay and coastal surface waters. These distribution patterns were similar to those of actual concentrations of tyrosine and tryptophan in total hydrolyzable amino acids (THAA) in DOM. Consequently, the tyrosine- and tryptophan-like fluorescence intensities were interpreted to be correlated to the concentrations of tyrosine and tryptophan, respectively, indicating that tyrosine and tryptophan were responsible for the protein-like fluorescence intensities of DOM. The protein-like fluorescence intensities were also correlated to the concentrations of THAA, suggesting that the dynamics of aromatic amino acids were similar to those of THAA. In addition, protein-like fluorescence intensities may be useful indicators as to the dynamics of not only aromatic amino acids but of THAA in bulk DOM as well. Comparison of the tyrosine- and tryptophan-like fluorescence intensities with the concentrations of aromatic amino acids and THAA suggests that the dissolved amino acids were components of relatively small peptides and not protein molecules.
Article
Amino acids, neutral sugars and amino sugars were analyzed to investigate the chemical composition and diagenetic processing of suspended particulate organic matter (POM, > 100 nm), high-molecular-weight dissolved organic matter (HMW DOM, 1–100 nm) and low-molecular-weight dissolved organic matter (LMW DOM, < 1 nm) at the time-series stations near Bermuda (BATS) and Hawaii (HOT). Differences between BATS and HOT were principally related to location-specific biogeochemical processes and water mass ventilation ages. Concentrations of amino acids, neutral sugar and amino sugars in unfiltered seawater sharply declined with depth at both stations, indicating an upper ocean source and rapid turnover of these components. The size distribution of organic matter was heavily skewed to smaller molecular sizes. Depth comparisons showed that larger size classes of organic matter were more efficiently removed than smaller size classes. Carbon-normalized yields of amino acids, neutral sugars and amino sugars decreased rapidly with depth and molecular size. Together these biochemicals accounted for 55% of organic carbon in surface POM but only 2% of the organic carbon in LMW DOM in deep water. Chemical compositions showed distinct differences between organic matter size classes indicating the extent of diagenetic processing increased with decreasing molecular size. These findings are consistent with the size-reactivity continuum model for organic matter in which bioreactivity decreases with decreasing molecular size and diagenetic processes lead to the formation of smaller components that are resistant to biodegradation. The data also provided evidence for a size-composition continuum. Carbon-normalized yields of amino acids, neutral sugars and amino sugars were sensitive indicators of diagenetic alterations. Diagenetic indicators based on amino acid compositions revealed distinct patterns for the North Pacific and Sargasso Sea possibly indicating the influence of varying sources or diagenetic processing.
Article
High-resolution fluorescence spectroscopy was used to characterize dissolved organic matter (DOM) in concentrated and unconcentrated water samples from a wide variety of freshwater, coastal and marine environments. Several types of fluorescent signals were observed, including humic-like, tyrosine-like, and tryptophan-like. Humic-like fluorescence consisted of two peaks, one stimulated by UV excitation (peak A) and one by visible excitation (peak C). For all samples, the positions of both excitation and emission maxima for peak C were dependent upon wavelength of observation, with a shift towards longer wavelength emission maximum at longer excitation wavelength and longer wavelength excitation maximum at longer emission wavelength. A trend was observed in the position of wavelength-independent maximum fluorescence () for peak C, with maximum at shorter excitation and emission wavelengths for marine samples than for freshwater samples. Mean positions of these maxima were: rivers = nm; coastal water = nm; marine shallow transitional = nm; marine shallow eutrophic = nm; and marine deep = nm. Differences suggest that the humic material in marine surface waters is chemically different from humic material in the other environments sampled. These results explain previous conflicting reports regarding fluorescence properties of DOM from natural waters and also provide a means of distinguishing between water mass sources in the ocean.
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Culture-dependent and -independent studies have found that prokaryotic assemblages are quite diverse in aquatic habitats and contain representatives of virtually all of the roughly 40 divisions of bacteria and the major archaeal groups found so far in the biosphere [1]. Fortunately, not all of these prokaryotic groups are abundant in the plankton nor important in all biogeochemical cycles. Autotrophic and heterotrophic bacteria dominate the prokaryotic biomass in surface waters, as Archaea appear to be abundant only in the plankton of the deep oceans [2]. Among the heterotrophic bacteria, the two most abundant groups are often the Proteobacteria and the subject of this review, the Cytophaga–Flavobacteria cluster (Table 1). View this table: 1 The relative abundance of the major heterotrophic bacterial groups in aquatic ecosystems, as determined by FISH with oligonucleotide probes This paper reviews recent studies that have applied molecular methods to examine uncultured Cytophaga–Flavobacteria in freshwaters and the oceans, with the ultimate goal of using this information to better understand the role of heterotrophic bacteria in carbon cycles and other biogeochemical processes. The importance of heterotrophic bacteria in biogeochemical processes is now well appreciated, but until recently geochemists and field-orientated microbial ecologists considered these microbes as if they were a single group, even though microbiologists have been accumulating for several years information about the taxonomic and phylogenetic make up (‘community structure’) of heterotrophic bacterial communities. Only recently, however, have microbial ecologists been able to link community structure with specific biogeochemical processes (‘function’) [3]. Here I summarize briefly our progress in these areas while discussing what we know about Cytophaga–Flavobacteria in aquatic habitats. This microbial group is a natural starting point because of its high abundance in many freshwater and marine systems. The Cytophaga–Flavobacteria cluster belongs to a diverse bacterial division that has been labeled differently over …
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Most of the oceanic reservoir of dissolved organic matter (DOM) is of marine origin and is resistant to microbial oxidation, but little is known about the mechanisms of its formation. In a laboratory study, natural assemblages of marine bacteria rapidly (in <48 hours) utilized labile compounds (glucose, glutamate) and produced refractory DOM that persisted for more than a year. Only 10 to 15% of the bacterially derived DOM was identified as hydrolyzable amino acids and sugars, a feature consistent with marine DOM. These results suggest that microbial processes alter the molecular structure of DOM, making it resistant to further degradation and thereby preserving fixed carbon in the ocean.