Phosphorus Release and Regeneration Following Laboratory Lysis of Bacterial Cells

The availability of phosphorus limits primary production in large regions of the oceans, and marine microbes use a variety of strategies to overcome this limitation. One strategy is the production of alkaline phosphatase (APase), which allows hydrolysis of larger dissolved organic phosphorus (DOP) compounds in the periplasm or at the cell surface for transport of orthophosphate into the cell. Cell lysis, driven by grazing and viral infection, releases phosphorus-containing cell components, along with active enzymes that could persist after lysis. The importance of this continued enzymatic activity for orthophosphate regeneration is unknown. We used three model bacteria – Escherichia coli K-12 MG1655, Synechococcus sp. WH7803, and Prochlorococcus sp. MED4 – to assess the impact of continued APase activity after cell lysis, via lysozyme treatment, on orthophosphate regeneration. Direct release of orthophosphate scaled with cell size and was reduced under phosphate-starved conditions where APase activity continued for days after lysis. All lysate incubations showed post-lysis orthophosphate generation suggesting phosphatases other than APase maintain activity. Rates of DOP hydrolysis and orthophosphate remineralization varied post-lysis among strains. Escherichia coli K-12 MG1655 rates of remineralization were 0.6 and 1.2 amol cell–1hr–1 under deplete and replete conditions; Synechococcus WH7803 lysates ranged from 0.04 up to 0.3 amol cell–1hr–1 during phosphorus deplete and replete conditions, respectively, while in Prochlorococcus MED4 lysates, rates were stable at 0.001 amol cell–1hr–1 in both conditions. The range of rates of hydrolysis and regeneration underscores the taxonomic and biochemical variability in the process of nutrient regeneration and further highlights the complexity of quantitatively resolving the major fluxes within the microbial loop.

Modeling silicate–nitrate–ammonium co-limitation of algal growth and the importance of bacterial remineralization based on an experimental Arctic coastal spring bloom culture study

Arctic coastal ecosystems are rapidly changing due to climate warming. This makes modeling their productivity crucially important to better understand future changes. System primary production in these systems is highest during the pronounced spring bloom, typically dominated by diatoms. Eventually the spring blooms terminate due to silicon or nitrogen limitation. Bacteria can play an important role for extending bloom duration and total CO2 fixation through ammonium regeneration. Current ecosystem models often simplify the effects of nutrient co-limitations on algal physiology and cellular ratios and simplify nutrient regeneration. These simplifications may lead to underestimations of primary production. Detailed biochemistry- and cell-based models can represent these dynamics but are difficult to tune in the environment. We performed a cultivation experiment that showed typical spring bloom dynamics, such as extended algal growth via bacterial ammonium remineralization, reduced algal growth and inhibited chlorophyll synthesis under silicate limitation, and gradually reduced nitrogen assimilation and chlorophyll synthesis under nitrogen limitation. We developed a simplified dynamic model to represent these processes. Overall, model complexity in terms of the number of parameters is comparable to the phytoplankton growth and nutrient biogeochemistry formulations in common ecosystem models used in the Arctic while improving the representation of nutrient-co-limitation-related processes. Such model enhancements that now incorporate increased nutrient inputs and higher mineralization rates in a warmer climate will improve future predictions in this vulnerable system.

Bioturbation of Thalassinoides from the Lower Cambrian Zhushadong Formation of Dengfeng area, Henan Province, North China

Bioturbation plays a critical role in sediment mixing and biogeochemical cycling between sediment and seawater. An abundance of bioturbation structures, dominated by Thalassinoides, occurs in carbonate rocks of the Cambrian Series 2 Zhushadong Formation in the Dengfeng area of western Henan Province, North China. Determination of elemental geochemistry can help to establish the influence of burrowing activities on sediment biogeochemical cycling, especially on changes in oxygen concentration and nutrient regeneration. Results show that there is a dramatic difference in the bioturbation intensity between the bioturbated limestone and laminated dolostone of the Zhushadong Formation in terms of productivity proxies (Baex, Cu, Ni, Sr/Ca) and redox proxies (V/Cr, V/Sc, Ni/Co). These changes may be related to the presence of Thalassinoides bioturbators, which alter the particle size and permeability of sediments, while also increase the oxygen concentration and capacity for nutrient regeneration. Comparison with modern studies shows that the sediment mixing and reworking induced by Thalassinoides bioturbators significantly changed the primary physical and chemical characteristics of the Cambrian sediment, triggering the substrate revolution and promoting biogeochemical cycling between sediment and seawater.

Estimating Nitrogen and Phosphorus Cycles in a Timber Reef Deployment Area

In an oligotrophic bay, Mitsu Bay, Japan, artificial timber reefs (ATRs) are deployed to increase fish production. In such man-made ecosystems, the biological activities of other organisms as well as the physical structures of ATRs could influence nutrient cycling. A pelagic–benthic coupling model expressing both phosphorus and nitrogen cycling was developed to investigate seasonal variation in the associated nutrients and their annual budget in the ATR areas and the entire bay system. The model consists of equations representing all the relevant physical and biological processes. The model reproduced the observed seasonal variations in dissolved inorganic P, ammonium, and nitrate concentrations that were low in spring and summer and high in autumn and winter. The internal regeneration rates of the nutrients were two times higher in the ATRs than in the bay area, so that fish production was predicted to be higher in the ATRs than in the bay area. Considering the inflows from the land and precipitation are quite low, nutrient regeneration is an important source of nutrients for the water in Mitsu Bay. ATR deployment could be an important local nutrient source in an oligotrophic bay, and could increase fish production.

Investigating equations for measuring dissolved inorganic nutrient uptake in oligotrophic conditions

ABSTRACTMultiple different equations have been used to quantify nutrient uptake rates from stable isotope tracer label incorporation experiments. Each of these equations implicitly assumes an underlying model for phytoplankton nutrient uptake behavior within the incubation bottle and/or pelagic environment. However, the applicability of different equations remains in question and uncertainty arising from subjective choices of which equation to use is never reported. In this study, I use two approaches to investigate the conditions under which different nutrient uptake equations should be used. First, I utilized a moderate-complexity pelagic ecosystem model that explicitly models the δ15N values of all model compartments (NEMURO+15N) to conduct simulated nitrate uptake and ammonium uptake incubations and quantify the accuracy of different nutrient uptake equations. Second, I used results of deckboard diel nutrient uptake experiments to quantify the biases of 24-h incubations relative to six consecutive 4-h incubations. Using both approaches, I found that equations that account for nutrient regeneration (i.e., isotope dilution) are more accurate than equations that do not, particularly when nutrient concentrations are low but uptake is relatively high. Furthermore, I find that if the goal is to estimate in situ uptake rates it is appropriate to use an in situ correction to standard equations. I also present complete equations for quantifying uncertainty in nutrient uptake experiments using each nutrient uptake equation and make all of these calculations available as Excel spreadsheets and Matlab scripts.

Nutrient regeneration and benthic fluxes in the Coastal Baltic and North Sea

<p>Sediments in the coastal ocean can play an important role in nutrient regeneration and in recharging the water column with dissolved inorganic nutrients. This function, however, depends on various variables, such as physical characteristics, but also on biological traits like fauna composition and activity. To unravel and quantify these effects, we investigated nutrient fluxes and nitrate stable isotope composition in water samples along a North Sea – Skagerrak – Baltic Sea gradient during the Maria S. Merian cruise MSM 50 in January 2016.</p><p>Especially in the North Sea and the Skagerrak region, d<sup>15</sup>N values of nitrate were unexpectedly high, suggesting that underlying sediments with relatively enriched isotope signatures were a source of nitrate. This nitrification signal, however, resembled an autumn situation rather than the expected winter values. Parallel sediment incubations confirm that the benthic rates of oxygen consumption and nutrient turnover were indeed very similar to respective rates in autumn and that the sediment was a source of recycled nitrate. From the North Sea towards the Baltic Sea, we found, in accordance with previous studies, a depletion in nitrate stable isotope values. This is indicative of different nitrate sources in the respective basins: in the North Sea region, N of anthropogenic origin leads to high N values in surface sediments and in newly generated nitrate. Due to a higher share of nitrogen fixation, the nitrogen stable isotope signal of surface sediments in the Baltic Sea was depleted, which in turn was mirrored in lower nitrate isotope values in the water column above the sediment.</p><p>Overall, the data highlight the importance of nitrate regeneration. Parallel flux measurements reveal that faunal activity shifts the nutrient balance from sequestration to regeneration. Seasonal differences enable us to unravel seasonal effects of fauna and microbiota on nutrient budgets.</p>

Functional traits of particle-associated microbial assemblages in the low-latitude Pacific Ocean

Background Organic particles are hotspots for microbial activity and serve as sites of organic matter mineralisation in the water column of marine systems. In nutrient-limited surface water, degradation of organic matter and nutrient regeneration by marine microbes is crucial. Although free-living (FL) bacteria vastly outnumber those on particles, particle-associated (PA) bacteria can reach locally higher concentrations. Accordingly, to achieve a better understanding of marine microbial ecosystems, it is important to elucidate the differences in not only microbial community structures, but also functional traits, between PA and FL environmental sample fractions. In a previous study, we demonstrated that the Genomaple (formerly MAPLE) system could successfully differentiate the functional potentials and diversity of contributors to each function in four metagenomic datasets generated by the Global Ocean Sampling expedition. Hence, we also used this system to highlight functional traits in PA microbial assemblages. Results The PA and FL fractions could be distinguished from one another by their taxonomic compositions, inferred from ribosomal proteins and relative abundance of module functions. Module functions that were more abundant among PA assemblages than FL assemblages were shared between both subtropical gyres, and their taxonomic compositions were similar. Bacterial transport systems associated with adhesive molecules used for forming microbial assemblages through particulate organic matter were more abundant in the PA fractions. Bacterial regulatory system elements for C 4 -dicarboxylate transport and B-vitamin biosynthesis were also abundant among PA assemblages, suggesting mutual relationships between bacteria and algae involved in exchange of nutrient sources. On the other hand, module functions related to amino acid biosynthesis and bacterial transport systems for inorganic nitrogen, phosphorus, and urea were significantly more abundant in the PA assemblages of more oligotrophic North and South Pacific subtropical gyres than eastern equatorial Pacific regions. Conclusions Comprehensive functional metagenomic analyses based on functional abundance revealed some notable functional traits in PA assemblages related to cell adhesion and nutrient acquisition, enabling the microbes to survive in subtropical regions that are more oligotrophic than the equatorial regions.

Isolation and Characterization of a Rhizobium Bacterium Associated with the Toxic Dinoflagellate Gambierdiscus balechii

ABSTRACTAlgae-bacteria associations are increasingly being recognized to be important in shaping the growth of both algae and bacteria. Bacteria belonging to order Rhizobiales are important symbionts of legumes often developing as nodules on plant roots, but have not been widely documented in association with algae. Here, we detected, isolated, and characterized a Rhizobium species from the toxic benthic dinoflagellate Gambierdiscus culture. The sequence of 16S rDNA showed 99% identity with that of Rhizobium rosettiformans. To further characterize the bacterium, we amplified and sequenced a cell wall hydrolase (CWH)-encoding gene; phylogenetic analysis indicated that this sequence was similar to the homologs of Martellela sp. and Hoeflea sp, of order Rhizobiales. We performed PCR using nifH primers to determine whether this bacterium can fix N2; however, the results of sequencing analysis showed that it was closer to chlorophyllide a reductase-encoding gene (bchX), which is similar to nifH. Results of 16S rDNA qPCR showed that compared to that in the early exponential phase, the abundance of this bacterium increased during the late exponential growth phase of Gambierdiscus. When the dinoflagellate culture was subjected to N limitation, the abundance of the bacterium represented by both 16S rDNA and CWH increased. Based on these results and published literature, it is apparent that this Rhizobium bacterium benefits from the association with Gambierdiscus by hydrolyzing and utilizing the extracellular organic matter exudates released by the dinoflagellate. This is the first report of Rhizobium species being associated with dinoflagellates, which will shed light on the algae-bacteria relationships.IMPORTANCEPhytoplankton are the undisputed primary producers in the aquatic ecosystems and contribute approximately half of the global net primary productivity.Dinoflagellates are one of the most important phytoplankton in the marine ecosystems. Commonly, they do not exist autonomously in the marine environment but rather co-live with many bacteria that interact with dinoflagellates, producing a dynamic microbial ecosystem. Their interactions play a major role in important processes such as carbon fluxes and nutrient regeneration in the ocean, ultimately influencing the global carbon cycle and the climate. Hence, there is a need to understand the association and relationships between dinoflagellates and bacteria. Here, we tried to elucidate these interactions through isolating and characterizing a bacterium from a benthic toxic dinoflagellate culture. Our study is the first report of such bacterium being recorded to be associated with a dinoflagellate in this genus, providing new insights into the dinoflagellate-bacteria association for future research.