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Microbial ecological functions are an emergent property of community composition. For some ecological functions, this link is strong enough that community composition can be used to estimate the quantity of an ecological function. Here, we apply random forest regression models to compare the predictive performance of community composition and environmental data for bacterial production (BP). Using data from two independent long-term ecological research sites-Palmer LTER in Antarctica and Station SPOT in California-we found that community composition was a strong predictor of BP. The top performing model achieved an R2 of 0.84 and RMSE of 20.2 pmol L-1 hr-1 on independent validation data, outperforming a model based solely on environmental data (R2 = 0.32, RMSE = 51.4 pmol L-1 hr-1). We then operationalized our top performing model, estimating BP for 346 Antarctic samples from 2015 to 2020 for which only community composition data were available. Our predictions resolved spatial trends in BP with significance in the Antarctic (P value = 1 × 10-4) and highlighted important taxa for BP across ocean basins. Our results demonstrate a strong link between microbial community composition and microbial ecosystem function and begin to leverage long-term datasets to construct models of BP based on microbial community composition.

Context: Metabolic balance determines whether an ecosystem acts as a source or sink of carbon dioxide (CO2) and considering that a substantial portion of inland aquatic ecosystems act as a source of CO2 to the atmosphere, it is important to highlight that there is still no agreement on how global change will affect the ecosystem metabolic-balance response. It then becomes more important to study the interactions between global-change drivers and aquatic metabolism. Aims: Assess possible shifts in ecosystem metabolic balance owing to global-change factors. Methods: Collapsed factorial designs and novel experimental units have been used to study responses to future conditions. Key results: In the study site, bacterial production was not affected by an increased temperature alone; however, increased nutrient availability may unmask UV or CO2 as a source of stress to bacteria. A synergistic effect between temperature and the combined effect of nutrients and CO2 on primary producers was also found. Conclusions: In future scenarios, some heterotrophic inland water ecosystems may shift from heterotrophic to autotrophic states and therefore act as CO2 sinks. Implications: This study provides a framework to support a deepening of knowledge on this topic. Many inland waters act as a source of carbon dioxide (CO2) to the atmosphere. The ecosystem metabolic balance determines this response, making it a key topic of study, including its interactions with drivers of global change to acknowledge future responses. In this study, new experimental units and novel collapsed factorial designs are employed to address the potential shift from source to sink of CO2 from inland freshwaters. [ABSTRACT FROM AUTHOR]

Environmental monitoring of the Russian sectors of the Baltic Sea was continued through three expeditions in 2023: cruise 55 of the R/V Akademik Sergei Vavilov (April) and cruises 54 and 55 of the R/V Akademik Boris Petrov (November and December, respectively). Seasonal quantitative estimates of hydrological–hydrochemical and hydrobiological parameters and carbon dioxide fluxes at the water–air interface were obtained, and the geological and geomorphological conditions of the study areas were refined. The influence of the Neva River on the eastern Gulf of Finland was stable in all seasons and could be traced at a distance of up to 30 nautical miles from Neva Bay. The Southeastern Baltic bottom layer experienced extensive hypoxia and mosaic euxinia. Significant aeration of bottom waters occurred in December due to the combined influence of seasonal convection and downwelling resulting from a series of storms. In both study areas, high values of integral primary production were obtained in April, which were two orders of magnitude higher than the December values. The concentration of chlorophyll a, accordingly, differed by an order of magnitude. The Gulf of Finland was an emitter of carbon dioxide into the atmosphere, especially in April, while the Southeastern Baltic absorbed carbon dioxide in April and was a zone of weak emissions in November and December. [ABSTRACT FROM AUTHOR]

Glucagon, a peptide hormone clinically used to treat acute hypoglycemia in diabetes patients, is readily degenerated by undergoing fibrillation under pharmaceutical conditions. Since glucagon is employed as a typical model system for structural investigation of amyloid fibril formation of proteins, production of recombinant glucagon is in demand to facilitate mutagenesis and isotope labeling for nuclear magnetic resonance (NMR) studies. In this study, we established a method to produce recombinant glucagon in Escherichia coli. Recombinant plasmids were constructed to express a maltose-binding protein-fused glucagon, which was cleaved by factor-Xa protease to yield glucagon peptide without any N-terminal extra residues. The final product was clearly identified and characterized by immunoblotting, mass spectrometry, circular dichroism spectroscopy, and backbone NMR assignments of the [13C/15N] isotope-enriched sample. Cellular activity of the recombinant glucagon in hepatocytes was confirmed by monitoring characteristic gene expressions. Site-directed mutagenesis was successfully performed using our recombinant production system. Our bacterial production system and the recombinant glucagon not only provide an economical route of glucagon manufacturing, but also enable NMR-based structural investigation of glucagon fibrillation. [Display omitted] • Bacterial production of a recombinant glucagon was established using Escherichia coli. • MBP used as a fusion tag was cleaved by factor-Xa to yield isolated glucagon. • Final product was validated by mass spectrometry and activity assay in hepatocytes. • Mutagenesis and isotope labeling were successful using the production system. • Backbone NMR assignments were completed by heteronuclear multidimensional NMR. [ABSTRACT FROM AUTHOR]

Marine environments wherein long-term microbial oxygen consumption exceeds oxygen replenishment can be associated with oxygen minimum zones (OMZ). The Bay of Bengal OMZ (BOB-OMZ) is one of the most intense OMZs globally. To assess the contribution of bacterial oxygen consumption to oxygen loss in BOB-OMZ, we measured bacterial production (BP), temperature, salinity, and dissolved oxygen (DO) in the whole water column. We then compared the estimated bacterial oxygen demand (BOD) with diapycnal oxygen supply (DOS) at depths of 50-200 m in the southern BOB in January 2020. The average BP was 3.53 ± 3.15 µmol C m-3 h-1 in the upper 200 m of four stations, which was lower than those reported in other tropical waters. The vertical distribution of BP differed between the open ocean and nearshore areas. In the open ocean, temperature and DO were the most important predictors for BP in the whole water column. In the nearshore areas, when DO increased sharply from the suboxic state, extremely high BP occurred at 200 m. The average estimated BOD/DOS could reach up to 153% at depths of 50-200 m, indicating advection and anticyclonic eddies probably are important DO replenishment pathways in the BOB. [ABSTRACT FROM AUTHOR]

Although single-chain variable fragment (scFv) is recognized as a highly versatile scaffold of recombinant antibody fragment molecules, its overexpression in Escherichia coli often leads to the formation of inclusion bodies. To address this issue, we devised and tested four different constructs, named v21, v22, v23 and v24, for producing anti-human epidermal growth factor receptor 2 (HER2) scFv. Among them, the v24 construct obtained from N-terminal fusion of maltose-binding protein (MBP) and subsequent tobacco etch virus protease (TEV) was identified as the most efficient construct for the production of anti-HER2 scFv. Aided by an MBP tag, high-yield soluble expression was ensured and soluble scFv was liberated in cells via autonomous proteolytic cleavage by endogenously expressed TEV. The isolated scFv containing a C-terminal hexahistidine tag was purified through a one-step purification via nickel-affinity chromatography. The purified scFv exhibited a strong (nanomolar Kd) affinity to HER2 both in vitro and in cells. Structural and functional stabilities of the scFv during storage for more than one month were also assured. Given the great utility of anti-HER2 scFv as a basic platform for developing therapeutic and diagnostic agents for cancers, the v24 construct and methods presented in this study are expected to provide a better manufacturing system for producing anti-HER2 scFv with various industrial applications. [ABSTRACT FROM AUTHOR]

It is widely accepted that in many aquatic ecosystems bacterioplankton is dependent on and regulated by organic carbon supplied by phytoplankton, leading to coupled algae-bacteria relationship. In this study, an in-depth analysis of this relationship has been carried out by combining two approaches: (i) a correlation analyses between heterotrophic bacterial production (BP) vs. primary production (PP) or algal excretion of organic carbon (EOC), (ii) the balance between bacterial carbon demands (BCD) and the supply of C as EOC, measured as BCD:EOC ratio. During the study period (2013–2016), the algae-bacteria relationship was constantly changing from a coupling in 2013, uncoupling in 2014 and 2015, and an incipient return to coupling (in 2016). Our results show that top-down control (bacterivory) by algal mixotrophy acts as a decoupling force since it provides a fresh C source different to algal EOC to satisfy bacterial carbon demands. Notably, a relationship between the BCD:EOC ratio and the ecosystem metabolic balance (Primary production (PP): respiration (R)) was found, suggesting that PP:R may be a good predictor of the algae-bacteria coupling. This analysis, including the comparison between basal and potential ecosystem metabolic balance, can be a tool to improve knowledge on the interaction between both biotics compartments, which the traditional analyses on coupling may not capture. [ABSTRACT FROM AUTHOR]

The structure and productivity of planktonic microbial communities in the ecosystems of the Siberian Arctic seas are significantly dependent on freshwater input. During the study, we determined the spatial distribution of the abundance, biomass, and production of heterotrophic bacterioplankton in the Western Laptev Sea on the transect from the Khatanga River estuary to the continental slope and assessed the impact of river freshwater discharge. The influence of fresh water on bacterioplankton was restricted mainly to Khatanga Bay (KHAB) and the transitional zone (TZ) and was poorly recognized in the Western shelf (WS) and continental slope (CS) areas. The total bacterial abundance decreased from KHAB to the CS. Particle-attached bacteria constituted on average 63.0% of the total abundance of bacterioplankton in KHAB and 1.0% at the CS. Average bacterial production in the water column was highest in KHAB (10.3 mg C m−3 d−1), decreasing towards the CS (0.7 mg C m−3 d−1). In KHAB and TZ, bacteria were the main component of the planktonic community (44−55%). These results show that at the end of the growing season, bacterial processes prevailed over autotrophic ones and contributed largely to the total biological carbon flux in the coastal ecosystem of the Western Laptev Sea. [ABSTRACT FROM AUTHOR]

Context: We studied the virus component in the microbial food-web in the tropical coastal Sunda Shelf waters. Aims: We investigated viral processes, including the lysogenic to lytic shift dynamics with seawater warming and nutrient enrichment. Methods: We sampled nearshore and offshore waters of Peninsular Malaysia to provide a natural trophic gradient for correlational analyses. We also conducted laboratory experiments to investigate the changes in virus production rates and lysogeny, when temperature (range: 25–37°C) and nutrient concentrations (range: 0.1–1.0× marine-broth concentration) were manipulated. Key results: Observations showed site-dependent differences in dissolved inorganic nutrient concentration, Chl- a (0.21–3.54 μg L−1) and bacterial abundance (4.09 × 105−9.41 × 105 cells mL−1), but not in viral abundance (measured as virus-like particles or VLP) (1.04 × 106−2.39 × 106 VLP mL−1) and virus production rates (0.59 × 105−4.55 × 105 VLP mL−1 h−1). From laboratory experiments, both warming and nutrient enrichment increased virus production (R 2 > 0.651), decreased lysogeny (R 2 > 0.743), and resulted in an increase of the viral lysis:bacterial production ratio, and a stronger viral control on bacterial production. Conclusions: Although both seawater warming and nutrient enrichment increased virus production and reduced lysogeny, nutrient enrichment was a more important factor. Implications: The increasing nutrient concentrations in these waters will increase virus production and virus top-down control of bacteria, and drive the ecosystem towards heterotrophy. Tropical coastal waters are experiencing warming and nutrient enrichment, and these environmental changes increased both bacterial and virus production. Nutrient enrichment increased virus production and resulted in a stronger virus top-down control on bacterial production. Therefore, eutrophication will drive the ecosystem towards heterotrophy. [ABSTRACT FROM AUTHOR]

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In this study, we examined the response of phytoplankton and heterotrophic bacteria to B12 amendments in microcosm experiments in the coastal southeastern Mediterranean Sea (SEMS) during the summer, where ambient levels of dissolved B12 ranged from as low as ∼2 pmol L−1 to 60 pmol L−1 (median 5.3 pmol L−1). Additions of B12 (20 pmol L−1) to surface seawater triggered a 4‐fold increase in NO3+NO2 uptake compared to unamended seawater, resulting in proliferation of mainly pico/nano‐eukaryotic phytoplankton (∼30%) and increase in primary and bacterial productivity (40%–50%). Complimentary experiments that tested the combined effects of nutrient (NO3 and PO4) and B12 additions suggest that phytoplankton were primarily NO3 and B12 co‐limited, whereas heterotrophic bacteria were PO4 and B12 co‐limited. These results provide valuable information about the marine distribution of nutrient limitation in low nutrients low chlorophyll (LNLC) environments such as the SEMS, and how bacterioplankton might respond to environmental perturbations. Plain Language Summary: Most biogeochemical studies have focused primarily on the effects of dissolved nitrate and orthophosphate on marine phytoplankton and bacterial productivity. However, vitamin B12 is also an important co‐factor for phytoplankton and bacteria, which has been far less investigated. These few studies showed that despite the very low concentrations of dissolved B12 in the marine environment, it has a strong influence on phytoplankton and bacterial productivity. Here, we followed phytoplankton and bacterial abundance and activity in response to B12 additions using high‐resolution daily measurements, and microcosm bioassays with additional nutrient simulations (nitrate, orthophosphate). Our study site was the coastal southeastern Mediterranean Sea, and the experiments were done during the summer when the most nutrient‐poor conditions prevail. Our results indicate that additions of B12 triggered a rapid increase in nitrate uptake, resulting in increased abundance of phytoplankton (mostly pico/nano‐eukaryotes) and photosynthesis rates. We also show that phytoplankton "need" both nitrate and vitamin B12 to proliferate, while bacteria require orthophosphate and B12 to support their growth. These results add to the current knowledge on the limitations of phytoplankton and bacteria in the coastal southeastern Mediterranean Sea and have implications for the whole coastal food‐web in this nutrient‐poor ecosystem. Key Points: Addition of B12 increased pico/nano‐eukaryotes abundance during the illuminated hours and of cyanobacteria during night‐timeB12 amendments accelerated NO3 uptake by phytoplankton, resulting in increased primary production ratesPhytoplankton were co‐limited by NO3 and B12 while heterotrophic bacteria were co‐limited by B12 and PO4 [ABSTRACT FROM AUTHOR]

The seasonal dynamics of production processes in the Baltic Sea are poorly studied. The aim of our research was to study the seasonal features of primary productivity (including the balance with bacterial production) and its redistribution in plankton in the southeastern part of the Baltic Sea in different seasons. More than 70% of primary production is formed in the 0–10 m layer (74–97% of the PP in the euphotic layer). In the same layer, PP accounted for almost 100% of the sum of primary and bacterial production in April and October, and almost 60% in June. Photosynthetic efficiency (PP/rETR) increased in June and October, demonstrating an increase in phytoplankton utilization of absorbed light energy. The depth-integrated values of PP, Chl a, bacterial, and phytoplankton biomasses were maximal in October. The maximum values of zooplankton biomass were determined in June, and they were significantly (5–14 times) higher than in other seasons. The maximum values of bacterial production were also in June. [ABSTRACT FROM AUTHOR]

In this work, potential (by the fluorescence method) and realized (by the radiocarbon method) phytoplankton primary production and the production of heterotrophic bacteria were determined in the euphotic zone of the seaward part of the Gdansk Bay of the Baltic Sea in summer and autumn. The maximum quantum efficiency of photosystem II of phytoplankton (Fv/Fm) varied significantly in depth in June (0.33–0.59), but was uniformly very high in October (0.68–0.71), which indicates a potentially more active state of early autumn phytoplankton. Integral primary production in October was almost two times higher than in June (633 and 375 mg C/m2 per day, respectively), while bacterial production was one-and-a-half times lower (239 and 371 mg C/m2 per day, respectively). In the upper tenth layer of the water column, autotrophic production (phytoplankton) only slightly exceeded heterotrophic (bacterial) production in June (63% of the total production) and dominated in October (92% of the total production). [ABSTRACT FROM AUTHOR]

Although single-chain variable fragment (scFv) is recognized as a highly versatile scaffold of recombinant antibody fragment molecules, its overexpression in Escherichia coli often leads to the formation of inclusion bodies. To address this issue, we devised and tested four different constructs, named v21, v22, v23 and v24, for producing anti-human epidermal growth factor receptor 2 (HER2) scFv. Among them, the v24 construct obtained from N-terminal fusion of maltose-binding protein (MBP) and subsequent tobacco etch virus protease (TEV) was identified as the most efficient construct for the production of anti-HER2 scFv. Aided by an MBP tag, high-yield soluble expression was ensured and soluble scFv was liberated in cells via autonomous proteolytic cleavage by endogenously expressed TEV. The isolated scFv containing a C-terminal hexahistidine tag was purified through a one-step purification via nickel-affinity chromatography. The purified scFv exhibited a strong (nanomolar Kd) affinity to HER2 both in vitro and in cells. Structural and functional stabilities of the scFv during storage for more than one month were also assured. Given the great utility of anti-HER2 scFv as a basic platform for developing therapeutic and diagnostic agents for cancers, the v24 construct and methods presented in this study are expected to provide a better manufacturing system for producing anti-HER2 scFv with various industrial applications.

In coral reefs, heterotrophic bacteria play an important role in driving carbon cycle and sustaining coral health. Bacterial production (BP), bacterial respiration (BR) and bacterial community composition (BCC) were determined in the Luhuitou fringing reef and the surrounding ocean in the northern South China Sea on a seasonal basis, in order to examine bacterial metabolic activity and effect of temperature on bacterial community in the fringing coral reef. Our results showed that higher BP (3.52–12.45 μg C L−1 d−1) and bacterial growth efficiency (0.16–0.28) and lower cellular BR (8.34–31.73 fg C cell−1 d−1) in the Luhuitou fringing reef than the surrounding ocean was more likely attributed to substrate availability. Enhanced dissolved organic nitrogen availability preferentially triggered the growth of bacteria with high nucleic acid content (HNA bacteria), which was most possibly responsible for high BP in the coral reef. Heterotrophic bacteria were more sensitive to temperature in the highly productive Luhuitou fringing reef than the surrounding ocean. Temperature shaped BCC by mediating enzymatic activity in the coral reef, likely triggering opportunistic infections. Warming might not only promote the growth of HNA bacteria and shift BCC in the coral reef, which was partly responsible for coral disease, but also reduce oxygen replenishment from the surface due to stratification and elevate the oxygen consumption owing to high BR, consequently threatening the survival of corals. Our findings helped to better understand how heterotrophic bacteria mediated the survival of corals in response to fluctuations of temperature. Plain Language Summary: This study examined regulation of bacterial metabolic activities and community composition by temperature by determining bacterial metabolism and community composition in a fringing reef over a seasonal basis. Labile dissolved organic matter released by reef benthos stimulated bacterial growth, enhancing bacterial production and growth efficiency in the coral reef. Bacteria were more sensitive to temperature in highly productive coral reef than the pristine surrounding ocean. An increase in temperature triggered the growth of metabolically active bacteria and shifted bacterial community composition in the coral reef, likely triggering opportunistic infections, and simultaneously elevated oxygen consumption owing to high bacterial respiration, threatening coral survivals. These findings improved our understanding of how global warming affects coral health. Key Points: The growth of metabolically active bacteria resulted in high bacterial production and growth efficiency in coral reefHeterotrophic bacteria were more sensitive to temperature in the highly productive coral reef than in the surrounding oceanSeasonal shifts in bacterial community composition were more profound in the coral reef than the surrounding ocean [ABSTRACT FROM AUTHOR]

Extensive oceanographic data sets were combined with microbiological parameters to elucidate the tight coupling between glacial meltwater and heterotrophic bacterial production (BP) on the Getz Ice Shelf (GtzIS) in the Amundsen Sea. BP in the eastern GtzIS (EG; 85.8 pM Leu. h−1), where basal glacier meltwater upwells, was significantly higher than BP measured in the western GtzIS (WG; 50.6 pM Leu. h−1) and the Amundsen Sea Polynya (ASP; 27.8 pM Leu. h−1). BP in the EG accounted for 49% of primary production, which was greater than that of the WG (10%) and ASP (9.2%). Enhanced BP in the eastern GtzIS was not coupled with phytoplankton biomass, but correlated significantly with the freshwater fraction containing meltwater‐derived dissolved organic carbon (MW‐DOC). These results suggest that warming‐induced glacier melting weakens carbon sequestration efficiency in Antarctic coastal waters by stimulating heterotrophic metabolism that converts MW‐DOC to CO2. Plain Language Summary: The Getz Ice Shelf (GtzIS) in the Amundsen Sea, the third‐largest ice shelf (34,018 km2) on the West Antarctic Ice Sheet, is regarded as a hot spot for producing large amount of glacier meltwater (144.9 ± 14 Gt yr−1). In general, the amount of dissolved organic carbon (DOC) from terrestrial sources is negligible in Antarctic waters, making DOC supplied by phytoplankton a major carbon source for heterotrophic bacteria growth. Although Antarctica's glacial ice shelves are presumably a large reservoir of organic carbon (ca. 5.5 Pg C), little is known about the effect of glacial melting on the supply of DOC available to heterotrophic bacteria. On the eastern GtzIS, where glacial meltwater upwells to the surface water column, heterotrophic bacteria production has no significant positive relationship with phytoplankton biomass, but is positively correlated with freshwater fraction. This suggests that DOC in glacial meltwater, rather than phytoplankton, provides DOC to support enhanced bacteria production. Our results imply that global warming–related increases in glacial meltwater may stimulate heterotrophic bacterial metabolism that respires DOC to CO2, thereby reducing carbon sequestration efficiency in Antarctic coastal waters. Key Points: Unlike the sea‐ice melting system, enhanced bacterial production (BP) in the eastern Getz Ice Shelf (GtzIS) was uncoupled with phytoplankton biomassDissolved organic carbon in glacier meltwater likely stimulates BP on the eastern GtzISWarming‐induced glacial melting may weaken carbon sequestration in the Antarctic Ocean by stimulating heterotrophic bacterial metabolism [ABSTRACT FROM AUTHOR]

The eastern North Atlantic region receives large Saharan dust deposition inputs, providing nutrients and trace metals to the surface waters. We assessed the effects of intense dust deposition on phytoplankton and bacteria cell abundances, metabolic activity, and community structure, along a surface productivity gradient in the Mauritanian-Senegalese upwelling system. Dust concentrations above 4 mg L-1 were added to triplicate microcosms in four bioassay experiments, each lasting three days, increasing nitrate, phosphate and, to a lesser extent, silicate seawater concentrations. Even though dust deposition enhanced both heterotrophic and photosynthetic activity, bacterial production responded faster and stronger than primary production, especially as oligotrophic conditions increased. Bacterial production rates in oligotrophic waters almost tripled one day after the enrichment. However, such favorable response could not be observed on the total organic carbon production until a lag phase of 2 days and whilst under moderate eutrophic conditions. Dust enrichment benefited the presence of certain planktonic groups over others according to their nutrient requirements. Indicator species analysis revealed that our dust-treated microcosms were consistently characterized by Raphid-pennate diatoms, as well as by Hyphomonas genus of Alphaproteobacteria and several species of Alteromonas Gammaproteobacteria. Yet, changes in microbial community structure and composition were primarily shaped by the starting conditions of each experiment. These findings indicate that increasing dust deposition events and the weakening of the Mauritanian-Senegalese upwelling system under climate change may result in a more heterotrophic system, particularly in oligotrophic waters, reducing its potential to function as an atmospheric carbon sink.

The structure and productivity of planktonic microbial communities in the ecosystems of the Siberian Arctic seas are significantly dependent on freshwater input. During the study, we determined the spatial distribution of the abundance, biomass, and production of heterotrophic bacterioplankton in the Western Laptev Sea on the transect from the Khatanga River estuary to the continental slope and assessed the impact of river freshwater discharge. The influence of fresh water on bacterioplankton was restricted mainly to Khatanga Bay (KHAB) and the transitional zone (TZ) and was poorly recognized in the Western shelf (WS) and continental slope (CS) areas. The total bacterial abundance decreased from KHAB to the CS. Particle-attached bacteria constituted on average 63.0% of the total abundance of bacterioplankton in KHAB and 1.0% at the CS. Average bacterial production in the water column was highest in KHAB (10.3 mg C m−3 d−1), decreasing towards the CS (0.7 mg C m−3 d−1). In KHAB and TZ, bacteria were the main component of the planktonic community (44−55%). These results show that at the end of the growing season, bacterial processes prevailed over autotrophic ones and contributed largely to the total biological carbon flux in the coastal ecosystem of the Western Laptev Sea.

Since it is known that hyaluronic acid contributes to soft tissue growth, elasticity, and scar reduction, different strategies of producing HA have been explored in order to satisfy the current demand of HA in pharmaceutical products and formulations. The current interest deals with production via bacterial and yeast fermentation and extraction from animal sources; however, the main challenge is the right extraction technique and strategy since the original sources (e.g., fermentation broth) represent a complex system containing a number of components and solutes, which complicates the achievement of high extraction rates and purity. This review sheds light on the main pathways for the production of HA, advantages, and disadvantages, along with the current efforts in extracting and purifying this high-added-value molecule from different sources. Particular emphasis has been placed on specific case studies attempting production and successful recovery. For such works, full details are given together with their relevant outcomes. [ABSTRACT FROM AUTHOR]

We investigated changes in heterotrophic bacterial metabolic activities and associated carbon cycles in response to a change in dominant phytoplankton communities during two contrasting environmental conditions in austral summer in the Amundsen Sea polynya (ASP), Antarctica: the closed polynya condition in 2014 (ANA04) and the open polynya condition in 2016 (ANA06). In ANA04, Phaeocystis antarctica predominated phytoplankton biomass, comprising 78% of total phytoplankton carbon biomass, whereas diatoms and Dictyocha speculum accounted for 45% and 48% of total phytoplankton carbon biomass, respectively, in ANA06. Bacterial production (BP) showed a significant positive correlation with only chlorophyll-a (Chl-a, rho = 0.66, p < 0.001) in P. antarctica-dominated ANA04, whereas there were significant positive relationships of BP with various organic carbon pools, such as chromophoric dissolved organic matter (CDOM, rho = 0.84, p < 0.001), Chl-a (rho = 0.59, p < 0.001), and dissolved organic carbon (DOC, rho = 0.51, p = 0.001), in ANA06 when diatoms and D. speculum co-dominated. These results indicate that BP depended more on DOC directly released from P. antarctica in ANA04, but was supported by DOC derived from various food web processes in the diatom-dominated system in ANA06. The BP to primary production (BP : PP) ratio was three-fold higher in P. antarctica-dominated ANA04 (BP: PP = 0.09), than in diatom- and D. speculum-co-dominated ANA06 (BP : PP = 0.03). These results suggested that the microbial loop is more significant in Phaeocystis-dominated conditions than in diatom-dominated conditions. In addition, the decreases in BP : PP ratio and bacterial respiration with increasing diatom proportion in the surface mixed layer indicated that the change from P. antarctica to diatom predominance enhanced biological carbon pump function by increasing particulate organic carbon export efficiency. Consequently, our results suggest that bacterial metabolic response to shifts in phytoplankton communities could ultimately affect larger-scale ecological and biogeochemical processes in the water column of the ASP.

Microbially induced carbonate precipitation (MICP) is a process that hydrolysis urea by microbial urease to fill the pore spaces of soil with induced calcium carbonate (CaCO3) precipitates, which eventually results in improved or solidified soil. This research explored the possibility of using dairy manure pellets (DMP) and palm oil mill effluent (POME) as alternative nutrient sources for Sporosarcina pasteurii cultivation and CaCO3 bioprecipitation. Different concentrations (20–80 g l−1) of DMP and POME were used to propagate the cells of S. pasteurii under laboratory conditions. The measured CaCO3 contents for MICP soil specimens that were treated with bacterial cultures grown in DMP medium (60%, w/v) was 15·30 ± 0·04 g ml−1 and POME medium (40%, v/v) was 15·49 ± 0·05 g ml−1 after 21 days curing. The scanning electron microscopy showed that soil treated with DMP had rhombohedral structure‐like crystals with smooth surfaces, whilst that of POME entailed ring‐like cubical formation with rough surfaces Electron dispersive X‐ray analysis was able to identify a high mass percentage of chemical element compositions (Ca, C and O), whilst spectrum from Fourier‐transform infrared spectroscopy confirmed the vibration peak intensities for CaCO3. Atomic force microscopy further showed clear topographical differences on the crystal surface structures that were formed around the MICP treated soil samples. These nutrient sources (DMP and POME) showed encouraging potential cultivation mediums to address high costs related to bacterial cultivation and biocementation treatment. [ABSTRACT FROM AUTHOR]

The effects of benthic dissolved organic carbon (DOC) flux on the dynamics of DOC in the deep continental margins (200 – 2000 m depth) is poorly understood. We investigated heterotrophic prokaryotes (hereafter bacteria) production (BP) and the bio-reactive properties of sediment-derived dissolved organic matter (SDOM) to elucidate microbially mediated cause-effect relationships regarding the rapid consumption of dissolved oxygen (DO) and accumulation of humic-like fluorescent DOM (FDOMH) in the deep-water column (750 – 2000 m depth range) of the Ulleung Basin (UB) in the East Sea. BP in the deep water (2.2 μmol C m-3 d-1) of the UB was among the highest reported for various deep-sea sites. The high DOC concentration (55 μM) likely supported the high BP seen in the deep-water column of the UB. Concentrations of DOC and C1 component of the FDOMH, which is indicative of microbial metabolic by-products, were 13-fold and 20-fold greater, respectively, in pore water than in the overlying bottom water, indicating that the sediment in the continental margins is a significant source of DOM in the overlying water column. Fine-scale water sampling revealed that BP near the sediment (0 – 30 m above the seafloor; 2.78 μmol C m-3 d-1) was 1.67 times higher than that measured in the water column above (30 – 100 m above the seafloor; 1.67 μmol C m-3 d-1). In addition, BP increased in the bottom water incubation amended with SDOM-containing pore water (PW). The results demonstrated that SDOM contains bio-reactive forms of DOM that stimulate heterotrophic microbial metabolism at the expense of oxygen in the bottom water layer. The accumulation of C1 component in both PW-amended and unamended bottom water incubation (i.e., without an extra DOM supply from sediment) further indicated that refractory DOM is produced autochthonously in the water column via heterotrophic metabolic activity. This explains in part the microbially mediated accumulation of excess FDOMH in the deep-water column of the UB. Overall results suggest that the benthic release of bio-reactive DOM may be of widespread significance in controlling microbial processes in the deep-water layer of marginal seas.

The northern slope water of the South China Sea (SCS) is oligotrophic. The regenerated nitrogen from dissolved organic nitrogen (DON) has been suggested to play a pivotal role in sustaining primary productivity; however, DON cycling has not been investigated there. Dissolved free amino acids (DFAAs) and polyamines (DFPAs) are two major groups of labile DON that are used rapidly by heterotrophic bacteria, and important in nitrogen cycling. Here, we measured turnover rates and concentrations of representative DFAAs (arginine and glutamic acid) and DFPAs (putrescine) in waters of the northern slope of the SCS, to estimate uptake rates and evaluate their potentials to fulfill carbon and nitrogen demands of bacterial production. Furthermore, homologs of genes encoding transporter systems for arginine (aotJ) and putrescine (potD/potF) were quantified in metagenomes from four depths at two sampling stations. The taxa encoding these genes were identified to gain insight into the composition of microbial communities potentially utilizing DFAAs and DFPAs. We found that uptake rates of two DFAAs and putrescine were more rapid than measured previously in seawater with similar environmental characteristics. The uptake of arginine and glutamic acids was estimated to account for 2.4-51% (19 ± 14%) and 2.7-59% (24 ± 20%) of bacterial carbon and nitrogen demand, respectively, and putrescine uptake contributed 4.4-100% (27 ± 33%) and 13-293% (80 ± 96%), respectively. Spatial variation in uptake rates indicated that biogeochemical cycling of DFAAs was distinct from that of DFPAs. Redundancy analysis and metagenomes demonstrated that environmental variables and distinction in bacterial assembleges using DFAAs and DFPAs could both affect their dynamics in the northern slope water of the SCS. [ABSTRACT FROM AUTHOR]

A multidisciplinary approach was used to study the impact of fish farming on coastal bacterial communities in the inner part of the Bay of Piran (northern Adriatic). Differences in bacterial abundance, production and the occurrence of selected bacterial groups were studied in the water column around the cage and at different distances from the centre of the fish cage towards the open water, i.e., reference marine station. We also examined the effect of fish feeding on the surrounding system in a short-term in situ experiment based on the simultaneous collection of seawater samples from different locations around the fish cage before and after feeding of fish. Our study suggests that fish feeding has a moderate short-term effect on water column parameters, including bacterial abundance and production, only at a limited distance from the fish cages. The nitrifying, ammonia-oxidizing bacterial groups, as determined by the fluorescent in situ hybridization method, were represented at a higher percentage in the seawater samples in the middle and around the fish cages. β- Proteobacteria, γ-Proteobacteria and the Cytophaga-Flavobacterium group were represented to a higher percentage at sampling sites in the middle of the Bay of Piran and at the reference marine station. The Vibrio group was detected at all sampling sites. The accumulation of organically enriched fish food and waste products released into the seawater during the short-term experiment resulted in a significant increase in particulate matter, orthophosphate and ammonium. In response to the increase in inorganic nutrients, we observed a significant increase in bacterial production, while no significant differences were observed in bacterial abundance in such short time.

The seasonal dynamics of production processes in the Baltic Sea are poorly studied. The aim of our research was to study the seasonal features of primary productivity (including the balance with bacterial production) and its redistribution in plankton in the southeastern part of the Baltic Sea in different seasons. More than 70% of primary production is formed in the 0–10 m layer (74–97% of the PP in the euphotic layer). In the same layer, PP accounted for almost 100% of the sum of primary and bacterial production in April and October, and almost 60% in June. Photosynthetic efficiency (PP/rETR) increased in June and October, demonstrating an increase in phytoplankton utilization of absorbed light energy. The depth-integrated values of PP, Chl a, bacterial, and phytoplankton biomasses were maximal in October. The maximum values of zooplankton biomass were determined in June, and they were significantly (5–14 times) higher than in other seasons. The maximum values of bacterial production were also in June.

The aim of this paper was to determine the abundance and secondary production by bacteria inhabiting the surface microlayer and subsurface water in a specific water basin, i.e., polluted estuarine harbour channel. In a 3-year seasonal cycle, the total number of bacteria and their biomass were higher in the surface microlayer (SML) 7.57 × 108cells dm−3 and 15.86 µg C dm−3 than in the subsurface water (SSW) 4.25 × 108cells dm−3 and 9.11 µg C dm−3 of the studied channel. The opposite relationship was noted in the level of the secondary production (SML—37.16 μg C dm−3 h−1, SSW—60.26 μg C dm−3 h−1) in this water basin. According to the analysed microbiological parameters, the total number of bacteria and secondary production varied along the horizontal profile in the water of the studied channel. The total number of bacteria and their secondary production showed the seasonal variation as well. [ABSTRACT FROM AUTHOR]

Temperate shelf seas are productive areas with the potential to export high quantities of particulate organic carbon (POC), as sinking particles, to the sediments or off‐shelf to the open ocean. The amount of carbon which can be exported depends partly on the amount of POC produced and on the remineralization processes occurring on the sinking material. Here, we assessed the relative seasonal importance of microbial respiration and bacterial production associated with suspended, slow‐ and fast‐sinking particle fractions. The three fractions were collected in the Celtic Sea above and below the seasonal thermocline in November 2014, April and July 2015 using Marine Snow Catchers. The slow‐sinking fraction had higher microbial respiration and bacterial production rates than the fast‐sinking fractions, and these two fractions sustained rates of microbial respiration and bacterial production between 1 and 3 orders of magnitude lower than the suspended fraction. This low contribution of the slow‐ and fast‐sinking fractions was consistent with their low contribution to the POC concentration at the two depths sampled. The POC‐specific respiration rates associated with the slow‐ and fast‐sinking fractions were low (median 0.17 and 0.08 d−1, respectively), indicating low‐sinking particle degradation. Our results indicate that ∼5% of the POC in surface waters can be exported below the thermocline. Key Points: Higher microbial respiration and bacterial production rates estimated in slow‐sinking compared to fast‐sinking fractions in shelf watersDue to the low number of particles in the fast‐sinking fraction, their contribution to water column metabolism was lowSlow‐sinking fraction made the greatest contribution to the potential export of particulate organic carbon to sediments or off‐shelf [ABSTRACT FROM AUTHOR]

Abstract Vanillin is the major component which is responsible for flavor and aroma of vanilla extract and is produced by 3 ways: natural extraction from vanilla plant, chemical synthesis and from microbial transformation. Current research was aimed to study bacterial production of vanillin from native natural sources including sewage and soil from industrial areas. The main objective was vanillin bio-production by isolating bacteria from these native sources. Also to adapt methodologies to improve vanillin production by optimized fermentation media and growth conditions. 47 soil and 13 sewage samples were collected from different industrial regions of Lahore, Gujranwala, Faisalabad and Kasur. 67.7% bacterial isolates produced vanillin and 32.3% were non-producers. From these 279 producers, 4 bacterial isolates selected as significant producers were; A3, A4, A7 and A10. These isolates were identified by ribotyping as A3 Pseudomonas fluorescence (KF408302), A4 Enterococcus faecium (KT356807), A7 Alcaligenes faecalis (MW422815) and A10 Bacillus subtilis (KT962919). Vanillin producers were further tested for improved production of vanillin and were grown in different fermentation media under optimized growth conditions for enhanced production of vanillin. The fermentation media (FM) were; clove oil based, rice bran waste (residues oil) based, wheat bran based and modified isoeugenol based. In FM5, FM21, FM22, FM23, FM24, FM30, FM31, FM32, FM34, FM35, FM36, and FM37, the selected 4 bacterial strains produced significant amounts of vanillin. A10 B. subtilis produced maximum amount of vanillin. This strain produced 17.3 g/L vanillin in FM36. Cost of this fermentation medium 36 was 131.5 rupees/L. This fermentation medium was modified isoeugenol based medium with 1% of isoeugenol and 2.5 g/L soybean meal. ech gene was amplified in A3 P. fluorescence using ech specific primers. As vanillin use as flavor has increased tremendously, the bioproduction of vanillin must be focused.

Biogeochemical responses to mixing were examined in two cruise surveys along a transect across the Kuroshio Current (KC) in May and July 2020. Two stations located at the South China Sea (SCS)–KC mixing and the KC waters were chosen for the diel study. In the euphotic zone (~100 m depth), the average values of nitrate (0.97–1.62 μM), chlorophyll-a (Chl-a, 0.36–0.40 mg/m3), and primary production (PP; 3.46 ± 1.37 mgC/m3/day) of the mixing water station (MWS) of the two cruises were several folds higher than those of the KC station (KCS; nitrate, 0.03–0.10 μM; Chl-a, 0.14–0.24 mg/m3; and PP, 0.91 ± 0.47 mgC/m3/day). In the July cruise, the maximal bacterial production (BP) at the MWS (3.31 mgC/m3/day) was 82% higher in comparison with that of the KCS (1.82 mgC/m3/day); and the readings of Chl-a showed no trend with BP in the oligotrophic KCS, but a positive relationship was found among these measurements at the mesotrophic MWS. This implies that the trophic status of the system might affect phytoplankton–bacteria interactions. The backward-trajectory analyses conducted by an observation-validated three-dimensional model identified that the prevailing southwest monsoon drove a northeastward “intrusion” of the SCS waters in July 2020, resulted in mixing between SCS and Kuroshio (KC) waters off the east coast of southern Taiwan. For the first time, this study demonstrates that the high biological biomass and activities that occur in the KC are induced by the northward intrusion of the SCS waters.

The process of chemosynthesis can represent an important source of organic matter and energy across the benthic zone. However, its detailed vertical distribution and importance in relation to other microbial processes are still poorly investigated in inland aquatic ecosystems. Here, we determined the rates of dark inorganic carbon fixation (DCF) compared to heterotrophic bacterial production (BP) and oxygen consumption (SOC) across a depth profile of oxic to anoxic sediments in the littoral zone of nine tropical lakes located in one of the most important coastal conservation areas, the Jurubatiba Sandbank National Park (Rio de Janeiro, Brazil). Rates of DCF were highly variable (means of 0.1–1.2 mmol C m−2 d−1) among the studied lakes, with mostly production occurring below 10 mm of sediment in the anoxic zone. Although presenting a relatively low contribution in relation to BP and SOC, our study showed extensive microbial metabolism in the anaerobic sediment below the top centimeter, highlighting the importance of studying microbial processes across depth at fine scales. To our knowledge, it is the first study to show detailed vertical DCF rates in coastal tropical lake sediments, thus contributing to a better comprehension of the microbial role in the biogeochemical cycles of aquatic systems. [ABSTRACT FROM AUTHOR]

The data obtained during the recent decades indicate large-scale climatic changes in the Arctic Ocean, especially in the Siberian shelf seas. The impact of shrinking of the Arctic ice cover on marine net primary production (PP) was mostly studied using satellite-derived estimates of chlorophyll-a (Chl a), sea surface temperature, and sea ice concentrations, as well as various modeling approaches. However, no data are available on the quantitative relations between phytoplankton production and heterotrophic bacterioplankton activity in the broadest and shallowest shelf of the World Ocean - the East Siberian Arctic seas (ESAS). In this paper we present a full set of in situ measurements of main PP and microbial heterotrophy characteristics required for better understanding and further validation of the satellite and modeling approaches. In September–October 2011, during the 57th cruise of RV Akademik M.A. Lavrent'ev , PP, bacterioplankton abundance (BA) and bacterioplankton production (BP), as well the rates of dark CO 2 assimilation (DCA) were determined in the Chukchi, East Siberian, and Laptev seas and in the Gulf of Anadyr of the Bering Sea (a total of 26 stations) by in situ measurements using radiolabeled bicarbonate. All three important production indicators exhibited significant variance within the studied water areas of the Arctic (РР from 0.98 to 54.7 μg C L−1 day−1), (ВР from 1.1 to 17.1 μg C L−1 day−1), and (DCA from 0.23 to 8.7 μg C L−1 day−1). The state of phyto- and bacterioplankton was determined by analysis of the BP/PP and DCA/PP ratios. Active photosynthesis with efficient incorporation of inorganic carbon into the biomass was observed in the Chukchi Sea coastal eastern waters and in the Gulf of Anadyr. On the contrary, the phytoplankton primary production was extremely low in oligotrophic basins of the East Siberian and Laptev seas, while the activity of heterotrophic bacterioplankton consuming organic matter of phytoplankton origin was relatively high. The data of direct measurements can be used for further adjustment of the indirect assessments of production obtained by satellite observations. Glossary East Siberian Arctic seas (ESAS), net primary production (PP), bacterioplankton abundance (BA), bacterial biomass (BB), bacterial production (BP), Arctic Ocean PP (AO-PP), organic matter (OM), dissolved organic matter (DOM), colored dissolved organic matter (CDOM), light CO 2 assimilation (LCA), dark (heterotrophic + chemotrophic) CO 2 assimilation (DCA), production indicators of the surface water layer (PP surf , DCA surf , BP surf), estimated production indicators for the entire depth of the sea (PP int , DCA int , BP int ; mg C m−2 day−1). [Display omitted] • The Arctic seas are characterized by high heterogeneity of phyto- and bacterioplankton activity. • In the Chukchi and Bering seas, autotrophic production is higher than heterotrophic. • In the East Siberian and Laptev Seas, heterotrophic production is similar and higher than autotrophic. • The balance of autotrophic and heterotrophic plankton activity determines the direction of CO 2 flow. [ABSTRACT FROM AUTHOR]

Coral releases mucus into the surrounding seawater, providing an important organic and nutrient source for bacteria in coral reef systems. Despite thorough investigation in previous studies, bacteria respiration and grazing mortality by nanoplankton in coral reef systems remain poorly understood. To understand organic matter cycle in reef systems, it is necessary to reveal how coral mucus influences the energy and material transfer efficiency of the microbial loop. Here, we examined the production and grazing mortality of bacteria using a dilution method and the respiration of bacteria by directly measuring oxygen consumption in Acropora mucus-supplemented seawater (MuSW) multiple times over several years. The mucus significantly enhanced the bacterial production in MuSW compared with that in seawater. Bacterial respiration in MuSW was also significantly higher than that in seawater (SW). Bacterial carbon demand in MuSW was also higher than that in SW; however, bacterial growth efficiency did not change significantly. These results suggest that coral mucus benefits both bacterial growth and respiration. On the other hand, bacterial grazing mortality was not significantly different between MuSW and SW, suggesting that coral mucus did not directly enhance the activity and/or growth of bacterial grazers. According to previous reports, nanoflagellate number increases in response to an increase in bacteria. This suggests that coral mucus would have an indirect and delayed impact on bacterial grazers, whereas it would have a direct and immediate impact on bacteria. This study highlights that coral mucus raises the level of bacterial activity and could drive matter cycles through the microbial loop in reef systems. • This study highlights the importance of coral mucus on microbial activity. • Coral mucus enhanced both bacterial production and respiration in seawater. • Coral mucus did not affect bacterial growth efficiency. • Coral mucus did not directly enhance activity of bacterial grazer in seawater. • Coral mucus would drive microbial loop by altering microbial activity in reef system. [ABSTRACT FROM AUTHOR]

Nanoflagellate grazing and viral lysis are the two main causes of mortality losses of marine bacterioplankton. Deciphering the mortality losses across the water column helps us understand their ecological and biogeochemical consequences. In this study, we implemented the two-point modified dilution method consisting of treatment of undiluted and 25% nanoflagellates and/or virus density at the surface (3 m), deep chlorophyll maximum (DCM), and the mesopelagic zone (300 m and 500 m deep) in the subtropical northwestern Pacific Ocean in summer. We found that the bacterial per capita growth (2.3 ± 0.6 d−1) and production (12.4 ± 6.9 μgC L−1 d−1) were significantly higher at the DCM layer than at the mesopelagic zone, possibly because of tight bacteria-phytoplankton coupling and trophic interactions between bacteria, nanoflagellates, and viruses. Further, we found that ∼70% of the bacterial mortality loss can be attributed to nanoflagellate grazing in the DCM layer, while most of the mortality loss in the surface and the mesopelagic zone can be attributed to viral lysis. We argue that while bacterial production is more efficiently transferred to higher trophic levels at the DCM layer, it is predominately recycled in the viral loop on the surface and the mesopelagic zone. Our results reveal the vertical variation of bacterial growth, production, mortality loss to nanoflagellate grazing, and viral lysis, from which we could deduct their depth-dependent impacts on carbon flux in the water column. Our study facilitates the understanding of the impacts of nanoflagellates and viruses on bacterioplankton and the bacteria-mediated biogeochemical cycling. • In the north Pacific, bacterial growth is higher at the deep chlorophyll a maximum layer in summer. • Bacterial mortality caused by nanoflagellate outweighs viral lysis in the eutrophic zone. • Virus induced mortality is the main mortality cause in the mesopelagic zone. • Impacts of nanoflagellates and viruses on bacterial production are depth-dependent. [ABSTRACT FROM AUTHOR]

The marine macroalgae Ulva sp. is considered an ecosystem engineer in rocky shores of temperate waters worldwide. Ulva sp. harbors a rich diversity of associated microbial epibionts, which are known to affect the algae's typical morphological development and 'health'. We examined the interaction between airborne microbes derived from atmospheric aerosols and Ulva ohnoi growth and physiological state. Specifically, we measured U. ohnoi growth rates and photosynthetic efficiency (Fv/Fm), alongside its microbial epibionts abundance, activity and diversity following dust (containing nutrients and airborne microorganisms) or UV-treated dust (only nutrients) amendments to filtered seawater. Parallel incubations with epibionts-free U. ohnoi (treated with antibiotics that removed the algae epibionts) were also tested to specifically examine if dust-borne microbes can replenish the epibiont community of U. ohnoi. We show that viable airborne microbes can restore U. ohnoi natural microbial epibionts communities, thereby keeping the seaweed alive and 'healthy'. These results suggest that microbes delivered through atmospheric aerosols can affect epiphyte biodiversity in marine flora, especially in areas subjected to high annual atmospheric dust deposition such as the Mediterranean Sea. Viable airborne microbes can restore U. ohnoi natural microbial epibionts communities, thereby keeping the seaweed alive and 'healthy'. [ABSTRACT FROM AUTHOR]

Aquifers are important reservoirs for organic carbon. A fundamental understanding of the role of groundwater ecosystems in carbon cycling, however, is still missing. Using sediment flow-through microcosms, long-term (171d) experiments were conducted to test two scenarios. First, aquifer sediment microbial communities received dissolved organic matter (DOM) at low concentration and typical to groundwater in terms of composition (DOM-1x). Second, sediments received an elevated concentration of DOM originating from soil (DOM-5x). Changes in DOM composition were analyzed via NMR and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Carbon production, physiological adaptations and biodiversity of groundwater, and sediment prokaryotic communities were monitored by total cell counts, substrate use arrays, and deep amplicon sequencing. The experiments showed that groundwater microbial communities do not react very fast to the sudden availability of labile organic carbon from soil in terms of carbon degradation and biomass production. It took days to weeks for incoming DOM being efficiently degraded and pronounced cell production occurred. Once conditioned, the DOM-1x supplied sediments mineralized 294(±230) μgC L−1sed d−1, 10-times less than the DOM-5x fed sediment communities [2.9(±1.1) mgC L−1sed d−1]. However, the overall biomass carbon production was hardly different in the two treatments with 13.7(±4.8) μgC L−1sed d−1 and 14.3(±3.5) μgC L−1sed d−1, respectively, hinting at a significantly lower carbon use efficiency with higher DOM availability. However, the molecularly more diverse DOM from soil fostered a higher bacterial diversity. Taking the irregular inputs of labile DOM into account, shallow aquifers are assumed to have a low resilience. Lacking a highly active and responsive microbial community, oligotrophic aquifers are at high risk of contamination with organic chemicals.

Dissolved primary production (DPP), particulate primaryproduction (PPP), and the subsequent bacterial production (BP) and respiration (BR) were reported for the first time in the NW Pacific. The study area of the subtropical southern East China Sea covers different water types, including oligotrophic Kuroshio and Taiwan Strait waters, as well as nutrient-rich China coastal and upwelled Kuroshio subsurface waters. On an areal basis, DPP and PPP ranged from 67–1649 and 160–1182 mgC m–2 d–1, respectively, showing high values in the upwelling area. The contribution of DPP to total primary production (percent extracellular release; PER) averaged 40.8 ± 12.2% with >50% in the upwelling stations. The BP and BR ranged from 48–245 and 709–2822 mgC m–2 d–1, respectively, showing patterns similar to those of primary production. Bacterial growth efficiency (BGE) averaged 5.7 ± 1.4%, representing the lower end of global ocean values. Phytoplankton and bacteria were well coupled in the upwelling area, whereas primary production could not sustain the bacterial carbon demand (BCD) at other stations. The slope of the log–log relationship between DPP and PPP was >1, indicating that the microbial loop may receive relatively less organic carbon supply in the future warmer, less productive ocean.

Aquifers are important reservoirs for organic carbon. A fundamental understanding of the role of groundwater ecosystems in carbon cycling, however, is still missing. Using sediment flow-through microcosms, long-term (171d) experiments were conducted to test two scenarios. First, aquifer sediment microbial communities received dissolved organic matter (DOM) at low concentration and typical to groundwater in terms of composition (DOM-1x). Second, sediments received an elevated concentration of DOM originating from soil (DOM-5x). Changes in DOM composition were analyzed via NMR and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Carbon production, physiological adaptations and biodiversity of groundwater, and sediment prokaryotic communities were monitored by total cell counts, substrate use arrays, and deep amplicon sequencing. The experiments showed that groundwater microbial communities do not react very fast to the sudden availability of labile organic carbon from soil in terms of carbon degradation and biomass production. It took days to weeks for incoming DOM being efficiently degraded and pronounced cell production occurred. Once conditioned, the DOM-1x supplied sediments mineralized 294(±230) μgC L−1sed d−1, 10-times less than the DOM-5x fed sediment communities [2.9(±1.1) mgC L−1sed d−1]. However, the overall biomass carbon production was hardly different in the two treatments with 13.7(±4.8) μgC L−1sed d−1 and 14.3(±3.5) μgC L−1sed d−1, respectively, hinting at a significantly lower carbon use efficiency with higher DOM availability. However, the molecularly more diverse DOM from soil fostered a higher bacterial diversity. Taking the irregular inputs of labile DOM into account, shallow aquifers are assumed to have a low resilience. Lacking a highly active and responsive microbial community, oligotrophic aquifers are at high risk of contamination with organic chemicals. [ABSTRACT FROM AUTHOR]

Although freshwater systems comprise a small portion of land surface, they play a pivotal role in landscape carbon (C) cycling. Carbon processing by heterotrophic bacteria is critical, contributing to ecosystem production and dissolved organic carbon (DOC) processing. Riverine bacterial C metabolism is related to a diversity of factors, including (1) physiochemical conditions and inorganic nutrient concentrations and (2) DOC quality and quantity; however, the relative importance of these factors in influencing C metabolism across arid fluvial networks remains equivocal. This study examined C metabolism by heterotrophic bacterioplankton in the Rio Grande drainage, an arid river network in Texas, USA. We examined spatial variation in physicochemical and inorganic nutrient conditions, bacterial C metabolism, and DOC lability across the drainage and assessed whether variation in bacterial C metabolism was more related to physicochemical–inorganic nutrient conditions or DOC quantity and lability. Across the drainage, hydrology and landscape position influenced physicochemical conditions, bacterial abundance, phytoplankton biomass, and bacterial C metabolism and the proportion of variation in bacterial C metabolism explained by physicochemical/inorganic nutrient and DOC quality–quantity gradients was approximately equal. Bacterial abundance and production were associated with greater NH4+ and DOC concentrations and phytoplankton biomass, whereas bacterial respiration and growth efficiency were driven by DOC color and suspended particulate concentrations. Results indicate that aspects of bacterial C metabolism are influenced by different environmental factors related to autochthonous and allochthonous inputs to riverine systems, which has implications for C transformation, sequestration, and transport to the ocean. [ABSTRACT FROM AUTHOR]

In Lake Biwa, the largest lake in Japan, external pollutant loads have decreased since the 1980s, leading to improved water quality, such as reduction in biochemical oxygen demand (BOD) and PO43− concentrations. We examined long-term variation of bacterial production (BP) under these environmental changes from 2016–2017 in the north basin of Lake Biwa. BP was estimated by measuring the incorporation of stable isotope 15N-labeled deoxyadenosine (15N-dA) from June 2016 and December 2017 and compared with measurements from 1986 and 1997–1998. In 1986, BP was measured by following 3H-labeled thymidine (3H-TdR) incorporation and in 1997–1998 by tracking bacterial abundance in incubations and calculating specific growth rates (μ). To allow direct comparison of 15N-dA and 3H-TdR incorporation rates, we determined a conversion factor. To estimate μ in 2016–2017, we determined a factor for converting 15N-dA incorporation to cell number increase. In 2016–2017, the 15N-dA incorporation rate ranged from 0.13 to 30.7 pmol l−1 h−1 and μ ranged from 0.016 to 0.70 day−1. BP values from 3H-TdR incorporation rates in 1986 and μ in 1997–1998 were 4.6 and 2.1 times BP values in 2016–2017, respectively, confirming the decrease in BP over the past 3 decades in Lake Biwa. Water quality data showed only low decrease rates for BOD and total phosphorus concentration from the 1980s, whereas the rate of decrease for PO43− concentrations was equivalent to that of BP. BP and decomposition of organic matter are known to be strongly P-limited in Lake Biwa. Our results suggest that the decrease in BP can be explained by a reduction in readily bioavailable PO43−. Organic phosphorus can also be an important P-source for BP under conditions with very low PO43− concentrations (nM), and changes in the bioavailability of organic phosphorus might have also regulated BP dynamics. [ABSTRACT FROM AUTHOR]

Bacterial production and the accompanying environmental factors were measured in the water columns of two Arctic fjords during the cruise in July and August 2013. Water samples were collected at six stations located in the central part of Hornsund and Kongsfjorden. In Hornsund, where average water temperatures were 1.25-fold lower than in Kongsfjorden, the bacterial production was twice as high (0.116 ± 0.102 vs 0.05 ± 0.03 mg C m−3 h−1). Statistical analysis indicated that chlorophyll a concentration itself was not a significant factor that affected bacterial production, in contrast to its decomposition product, pheophytin, originating from senescent algal cells or herbivorous activity of zooplankton. Single and multiple regression analysis revealed that water temperature, dissolved organic carbon (DOC), and pheophytin concentration were the main factors affecting bacterial production in both fjords.

Cadaverine, a natural polyamine with multiple bioactivities that is widely distributed in prokaryotes and eukaryotes, is becoming an important industrial chemical. Cadaverine exhibits broad prospects for various applications, especially as an important monomer for bio-based polyamides. Cadaverine-based polyamide PA 5X has broad application prospects owing to its environmentally friendly characteristics and exceptional performance in water absorption and dimensional stability. In this review, we summarize recent findings on the biosynthesis, metabolism, and physiological function of cadaverine in bacteria, with a focus on the regulatory mechanism of cadaverine synthesis in Escherichia coli (E. coli). We also describe recent developments in bacterial production of cadaverine by direct fermentation and whole-cell bioconversion, and recent approaches for the separation and purification of cadaverine. In addition, we present an overview of the application of cadaverine in the synthesis of completely bio-based polyamides. Finally, we provide an outlook and suggest future developments to advance the production of cadaverine from renewable resources.

ABSTRACT In this study, a strain of SAR11 subgroup IIIa (termed HIMB114) was grown in seawater-based batch and continuous culture in order to quantify cellular features and metabolism relevant to SAR11 ecology. We report some of the first direct measurements of cellular elemental quotas for nitrogen (N) and phosphorus (P) for SAR11, grown in batch culture: 1.4 ± 0.9 fg N and 0.44 ± 0.01 fg P, respectively, that were consistent with the small size of HIMB114 cells (average volume of 0.09 μm3). However, the mean carbon (C) cellular quota of 50 ± 47 fg C was anomalously high, but variable. The rates of phosphate (PO43−) uptake measured from both batch and continuous cultures were exceptionally slow: in chemostats growing at 0.3 day−1, HIMB114 took up 1.1 ± 0.3 amol P cell−1 day−1, suggesting that

Phytoplankton and heterotrophic bacteria rely on a suite of inorganic and organic macronutrients to satisfy their cellular needs. Here, we explored the effect of dissolved inorganic phosphate (PO4) and several dissolved organic molecules containing phosphorus [ATP, glucose-6-phosphate, 2-aminoethylphosphonic acid, collectively referred to as dissolved organic phosphorus (DOP)], on the activity and biomass of autotrophic and heterotrophic microbial populations in the coastal water of the southeastern Mediterranean Sea (SEMS) during summertime. To this end, surface waters were supplemented with PO4, one of the different organic molecules, or PO4 + ATP, and measured the PO4 turnover time (Tt), alkaline phosphatase activity (APA), heterotrophic bacterial production (BP), primary production (PP), and the abundance of the different microbial components. Our results show that PO4 alone does not stimulate any significant change in most of the autotrophic or heterotrophic bacterial variables tested. ATP addition (alone or with PO4) triggers the strongest increase in primary and bacterial productivity or biomass. Heterotrophic bacterial abundance and BP respond faster than phytoplankton (24 h post addition) to the various additions of DOP or PO4 + ATP, followed by a recovery of primary productivity (48 h post addition). These observations suggest that both autotrophic and heterotrophic microbial communities compete for labile organic molecules containing P, such as ATP, to satisfy their cellular needs. It also suggests that SEMS coastal water heterotrophic bacteria are likely C and P co-limited.

Current research into bacterial dynamics on the Greenland Ice Sheet (GrIS) is biased toward cryoconite holes, despite this habitat covering less than 8% of the ablation (melt) zone surface. In contrast, the expansive surface ice, which supports wide-spread Streptophyte micro-algal blooms thought to enhance surface melt, has been relatively neglected. This study aims to understand variability in bacterial abundance and production across an ablation season on the GrIS, in relation to micro-algal bloom dynamics. Bacterial abundance reached 3.3 ± 0.3 × 105 cells ml−1 in surface ice and was significantly linearly related to algal abundances during the middle and late ablation periods (R2 = 0.62, p < 0.05; R2 = 0.78, p < 0.001). Bacterial production (BP) of 0.03–0.6 μg C L−1 h−1 was observed in surface ice and increased in concert with glacier algal abundances, indicating that heterotrophic bacteria consume algal-derived dissolved organic carbon. However, BP remained at least 28 times lower than net primary production, indicating inefficient carbon cycling by heterotrophic bacteria and net accumulation of carbon in surface ice throughout the ablation season. Across the supraglacial environment, cryoconite sediment BP was at least four times greater than surface ice, confirming that cryoconite holes are the true “hot spots” of heterotrophic bacterial activity.