Contrasting patterns of carbon cycling and dissolved organic matter processing in two phytoplankton–bacteria communities

Microbial consumption of phytoplankton-derived organic carbon in the pelagic food web is an important component of the global C cycle. We studied C cycling in two phytoplankton–bacteria systems (non-axenic cultures of a dinoflagellate Apocalathium malmogiense and a cryptophyte Rhodomonas marina) in two complementary experiments. In the first experiment we grew phytoplankton and bacteria in nutrient-replete conditions and followed C processing at early exponential growth phase and twice later when the community had grown denser. Cell-specific primary production and total community respiration were up to 4 and 7 times higher, respectively, in the A. malmogiense treatments. Based on the optical signals, accumulating dissolved organic C (DOC) was degraded more in the R. marina treatments, and the rate of bacterial production to primary production was higher. Thus, the flow of C from phytoplankton to bacteria was relatively higher in R. marina treatments than in A. malmogiense treatments, which was further supported by faster 14C transfer from phytoplankton to bacterial biomass. In the second experiment we investigated consumption of the phytoplankton-derived DOC by bacteria. DOC consumption and transformation, bacterial production, and bacterial respiration were all higher in R. marina treatments. In both experiments A. malmogiense supported a bacterial community predominated by bacteria specialized in the utilization of less labile DOC (class Bacteroidia), whereas R. marina supported a community predominated by copiotrophic Alpha- and Gammaproteobacteria. Our findings suggest that large dinoflagellates cycle relatively more C between phytoplankton biomass and the inorganic C pool, whereas small cryptophytes direct relatively more C to the microbial loop.

Contrasting patterns of carbon cycling and DOM processing in two phytoplankton-bacteria communities

Microbial consumption of phytoplankton-derived organic carbon in the pelagic food web is an important component of the global C cycle. We studied C cycling in two phytoplankton-bacteria systems (non-axenic cultures of a dinoflagellate Apocalathium malmogiense and a cryptophyte Rhodomonas marina) in two experiments. In the first experiment we grew phytoplankton and bacteria in nutrient replete conditions and followed C processing at early exponential growth phase and at two later phases. Primary production and total community respiration were up to 4 and 7 times higher, respectively, in the A. malmogiense treatments. Based on the optical signals, accumulating dissolved organic C (DOC) was degraded more in the R. marina treatments and the rate of bacterial production to primary production was higher. Thus, the flow of C from phytoplankton to bacteria was relatively higher in R. marina treatments than in A. malmogiense treatments which was further supported by faster 14C transfer from phytoplankton to bacterial biomass. In the second experiment we investigated consumption of the phytoplankton-derived DOC by bacteria. DOC consumption and transformation, bacterial production and bacterial respiration were all higher in R. marina treatments. In both experiments A. malmogiense supported a bacterial community predominated by bacteria specialized in the utilization of less labile DOC (class Bacteroidia) whereas R. marina supported a community predominated by copiotrophic Alpha- and Gammaproteobacteria. Our findings suggest that large dinoflagellates cycle relatively more C between phytoplankton biomass and the inorganic C pool whereas small cryptophytes direct relatively more C to the microbial loop.

Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria

Gut microbial transformations of flavonoids, an enormous class of polyphenolic compounds abundant in plant-based diets, are closely associated with human health. However, the enzymes that initiate the gut microbial metabolism of flavones and flavonols, the two most abundant groups of flavonoids, as well as their underlying molecular mechanisms of action remain unclear. Here, we discovered a flavone reductase (FLR) from the gut bacterium, Flavonifractor plautii ATCC 49531 (originally assigned as Clostridium orbiscindens DSM 6740), which specifically catalyses the hydrogenation of the C2–C3 double bond of flavones/flavonols and initiates their metabolism as a key step. Crystal structure analysis revealed the molecular basis for the distinct catalytic property of FLR. Notably, FLR and its widespread homologues represent a class of ene-reductases that has not been previously identified. Genetic and biochemical analyses further indicated the importance of FLR in gut microbial consumption of dietary and medicinal flavonoids, providing broader insight into gut microbial xenobiotic transformations and possible guidance for personalized nutrition and medicine.

A unified theory for organic matter accumulation

Organic matter constitutes a key reservoir in global elemental cycles. However, our understanding of the dynamics of organic matter and its accumulation remains incomplete. Seemingly disparate hypotheses have been proposed to explain organic matter accumulation: the slow degradation of intrinsically recalcitrant substrates, the depletion to concentrations that inhibit microbial consumption, and a dependency on the consumption capabilities of nearby microbial populations. Here, using a mechanistic model, we develop a theoretical framework that explains how organic matter predictably accumulates in natural environments due to biochemical, ecological, and environmental factors. Our framework subsumes the previous hypotheses. Changes in the microbial community or the environment can move a class of organic matter from a state of functional recalcitrance to a state of depletion by microbial consumers. The model explains the vertical profile of dissolved organic carbon in the ocean and connects microbial activity at subannual timescales to organic matter turnover at millennial timescales. The threshold behavior of the model implies that organic matter accumulation may respond nonlinearly to changes in temperature and other factors, providing hypotheses for the observed correlations between organic carbon reservoirs and temperature in past earth climates.

A unified theory for organic matter accumulation

Organic matter constitutes a key reservoir in global elemental cycles. However, our understanding of the dynamics of organic matter and its accumulation remains incomplete. Seemingly disparate hypotheses have been proposed to explain organic matter accumulation: the slow degradation of intrinsically recalcitrant substrates, the depletion to concentrations that inhibit microbial consumption, and a dependency on the consumption capabilities of nearby microbial populations. Here, using a mechanistic model, we develop a theoretical framework that explains how organic matter predictably accumulates in natural environments due to biochemical, ecological, and environmental factors. The new framework subsumes the previous hypotheses. Changes in the microbial community or the environment can move a class of organic matter from a state of functional recalcitrance to a state of depletion by microbial consumers. The model explains the vertical profile of dissolved organic carbon in the ocean and connects microbial activity at subannual timescales to organic matter turnover at millenial timescales. The threshold behavior of the model implies that organic matter accumulation may respond nonlinearly to changes in temperature and other factors, providing hypotheses for the observed correlations between organic carbon reservoirs and temperature in past earth climates.

Use of a Novel Biopellet to Treat Total Petroleum Hydrocarbon Contaminated Groundwater

Conventional pump-and-treat strategies for dealing with groundwater contamination are both energy- and time-consuming. Potential passive biological techniques are of interest to remedy the massive volume of total petroleum hydrocarbon (TPH)-contaminated groundwater worldwide. In this study, novel biopellets made of TPH-acclimated microbes, fermented fruit peel materials, and CaO2 recycled from eggshells were manufactured to treat TPH-contaminated groundwater. The biopellets provided 56 mg of oxygen and achieved a C:N:P ratio by weight of 10:4:1. Moreover, each biopellet was capped with alginate to prolong its floating time in water to 25 days. The mimicked groundwater spiked with 500 mg/L diesel TPHs (TPHd) was treated using our novelly manufactured biopellets. After 8 days of treatment, results showed a 98.8% removal of spiked TPHd at a rate of 64.1 mg/L per day, with a microbial count that increased from nearly zero to 1.0 × 107 CFU/mL. The residual TPHd constituents were mainly C13–C18. Furthermore, microbial consumption of N, P, and oxygen was noted during the 8-day period of TPHd removal. As the TPHd level increased to 1500 mg/L, the removal rate reached 45 mg/L per day, and all TPHd had been removed after 22 days.

Abiotic hydrogen (H2) sources and sinks near the Mid-Ocean Ridge (MOR) with implications for the subseafloor biosphere

Free hydrogen (H2) is a basal energy source underlying chemosynthetic activity within igneous ocean crust. In an attempt to systematically account for all H2within young oceanic lithosphere (<10 Ma) near the Mid-Ocean Ridge (MOR), we construct a box model of this environment. Within this control volume, we assess abiotic H2sources (∼6 × 1012mol H2/y) and sinks (∼4 × 1012mol H2/y) and then attribute the net difference (∼2 × 1012mol H2/y) to microbial consumption in order to balance the H2budget. Despite poorly constrained details and large uncertainties, our analytical framework allows us to synthesize a vast body of pertinent but currently disparate information in order to propose an initial global estimate for microbial H2consumption within young ocean crust that is tractable and can be iteratively improved upon as new data and studies become available. Our preliminary investigation suggests that microbes beneath the MOR may be consuming a sizeable portion (at least ∼30%) of all produced H2, supporting the widely held notion that subseafloor microbes voraciously consume H2and play a fundamental role in the geochemistry of Earth’s ocean–atmosphere system.

Linking microbial genomes with their potential to degrade terrestrial organic matter in the Amazon River

Rivers connect the carbon cycle in land with that in aquatic ecosystems by transporting and transforming terrestrial organic matter (TeOM). The Amazon River receives huge loads of TeOM from the surrounding rainforest, promoting a substantial microbial heterotrophic activity and consequently, CO2 outgassing. In the Amazon River, microbes degrade up to 55% of the lignin present in the TeOM. Yet, the main microbial genomes involved in TeOM degradation were not known. Here, we characterize 51 population genomes (PGs) representing some of the most abundant microbes in the Amazon River deriving from 106 metagenomes. The 51 reconstructed PGs are among the most abundant microbes in the Amazon River, and 53% of them are not able to degrade TeOM. Among the PGs capable of degrading TeOM, 20% were exclusively cellulolytic, while the others could also oxidize lignin. The transport and consumption of lignin oxidation byproducts seemed to be decoupled from the oxidation process, being apparently performed by different groups of microorganisms. Altogether, based on our findings, we suggest a new priming effect model that explains the quick turnover of TeOM as a product of the microbial consumption of lignin-derived aromatic compounds produced by lignin oxidation, reducing the inhibition of cellulose degradation and ensuring structural carbon and energy for cell growth. By connecting the genomic features of abundant microbes in the Amazon River with the degradation of recalcitrant TeOM, we contribute to increase our understanding of the rapid consumption of recalcitrant compounds in this ecosystem.

Acrylic acid and related dimethylated sulfur compounds in the Bohai and Yellow seas during summer and winter

Spatiotemporal distributions of dissolved acrylic acid (AAd) and related biogenic sulfur compounds including dimethylsulfide (DMS) and dissolved and total dimethylsulfoniopropionate (DMSPd and DMSPt) were investigated in the Bohai Sea (BS) and Yellow Sea (YS) during summer and winter. AAd and DMS production from DMSPd degradation and AAd degradation were analyzed. Significant seasonal variations in AAd and DMS(P) were observed. AAd exhibited similar distributions during summer and winter; i.e., relatively high values of AAd occurred in the BS and the northern YS, and the concentrations decreased from inshore to offshore areas in the southern YS. Due to strong biological production from DMSP and abundant terrestrial inputs from rivers in summer, the AAd concentrations in the surface seawater during summer (30.01 nmol L−1) were significantly higher than those during winter (14.98 nmol L−1). The average concentration sequence along the transects during summer (AAd > DMSPt > DMS > DMSPd) showed that particulate DMSP (DMSPp) acted as a DMS producer and that terrestrial sources of AAd were present; in contrast, the sequence in winter was AAd > DMSPt > DMSPd > DMS. High values of AAd and DMS(P) were mostly observed in the upper layers, with occasional high values at the bottom. High AAd concentrations in the porewater, which could be transported to the bottom water, might result from the cleavage of intracellular DMSP and reduce bacterial metabolism in sediments. In addition, the production and degradation rates of biogenic sulfur compounds were significantly higher in summer than in winter, and the removal of AAd was primarily attributed to microbial consumption. Other sources of AAd existed aside from the production from DMSPd.