Carbon Source Availability Research Articles

Spatial and seasonal variability of the carbon isotopic signature of Daphnia and their ephippia in four French lakes: Implications for the study of carbon transfers in lake food webs

Abstract Carbon isotope analysis (δ13C) of Daphnia resting‐eggs (ephippia) in sedimentary records can be used to reconstruct past carbon transfers in pelagic food webs in lakes. However, there may be seasonal variability of cladoceran δ13C and ephippia production that could affect their use as palaeoecological indicators of pelagic carbon transfers. This is particularly likely in stratified lakes where availability of different pelagic carbon sources is seasonal. In addition, there are currently no studies on spatial variability of ephippia δ13C in deep areas of lakes and its implications for sampling strategies in paleolimnological studies. Four French lakes were sampled for over a year to evaluate seasonal variation of the carbon sources consumed by Daphnia using analyses of the Daphnia carbon isotope signature (δ13CDaphnia) and suspended organic matter signature (δ13Cseston). Daphnia ephippia were also collected from surface sediments at maximum depth in the four lakes. Ephippia signatures (δ13Cephippia) were compared to the δ13CDaphnia to evaluate ephippia production periods and the implications for the use of δ13Cephippia in trophic functioning studies. In addition, spatial variability of δ13CDaphnia among the four lakes and the variability of δ13Cephippia in the deep area of one lake were assessed to determine the relevance of a single sampling point in the context of paleolimnological studies. A similar pattern was observed in all four lakes: δ13CDaphnia was close to δ13Cseston during the summer stratification period, but δ13CDaphnia became much lower than δ13Cseston after the autumnal turnover. Ephippia seem to be produced either during the summer stratification period or after autumnal turnover depending on the lake. No spatial variability was observed among the sampling points in δ13CDaphnia in the four lakes, and δ13Cephippia seems to be spatially randomly distributed in the deep zone of the studied lake. In the four lakes, summer δ13CDaphnia values were never below −40‰, reflecting mainly the consumption of phytoplankton, which in turn uses varying amounts of CO2 from respiration (depending on the lake). After autumnal turnover, the δ13CDaphnia values reached values far below −40‰, reflecting the transfer of a non‐negligible part of C‐CH4 for three of the lakes. Seasonal stratification and turnover mechanisms seem to influence the availability of carbon sources in the pelagic compartment of the four lakes. This study shows that the timing of ephippia production affects the information provided by δ13Cephippia due to seasonal differences in the mechanisms (stratification, autumnal turnover) that determine which carbon sources are available in the pelagic compartment. Therefore, using δ13Cephippia to study past pelagic transfers of carbon in stratified lakes may entail uncertainty if used alone and requires multi‐proxy studies. Finally, δ13Cephippia appear to be homogeneously distributed in the deepest area of a medium‐sized, single basin. A single core retrieved from the deepest part of the lake should therefore provide a representative sample of the ephippia produced in a lake.

Structural analysis of microbiomes from salt caverns used for underground gas storage

Salt caverns are a safe and well-proven reservoir for large-scale natural gas storage and hence, a potential hydrogen storage. Contrary to natural gas, hydrogen is a favorable energy source for many microorganisms. Microorganisms are ubiquitously abundant in the upper lithosphere and therefore expected to be present also in subsurface geological formations potentially selected for H2 storage, such as salt caverns. Thus, future salt cavern hydrogen storage requires monitoring of the cavern microbiome, to evaluate and prevent unwanted microbial activities. In this study, we analyzed the microbiomes of brines sampled from the bottom of five German natural gas storage caverns. All brines were colonized by microorganisms in considerable cell numbers ranging from 2 × 106 cells ml−1 to 7 × 106 cells ml−1. The structures of the microbiomes were characterized by 16S rRNA gene amplicon sequencing. A core community detected in all five studied caverns consists of members affiliated to the Halobacteria, Halanaerobiales and Balneolales. Further, a phylotype belonging to the extremely halophilic, lithoautotrophic and sulfate-reducing genus Desulfovermiculus was found. Examination of microbial activity also included measuring hydrochemical parameters in order to assess the salt concentrations and the availability of nutrients and potential microbial carbon sources or metabolites. NaCl (4.7 M) was the main salt and sulfate (at average 40.8 mM) the main electron acceptor; methanol (up to 37.5 mM) and ethanol (up to 6.9 mM) were of anthropogenic origin and found in higher concentrations. Some putative microbial metabolites were found in lower concentrations (butyrate, ≤0.7 mM; formate, ≤0.08 mM; acetate, ≤0.5 mM; lactate, ≤0.06 mM); their potential relation to microbial activity is discussed. We propose a guideline for sampling and subsequent chemical and molecular biological analysis for future characterization of microbial communities of salt cavern brines.

Mangrove macroalgae increase their growth under ocean acidification: A study with Bostrychia (Rhodophyta) haplotypes from different biogeographic provinces

Increasing oceanic CO2 has caused a decrease in oceanic pH, a process termed ocean acidification (OA). OA may benefit fleshy macroalgae due to the increased availability of inorganic carbon sources for photosynthesis since they are tolerant of decreases in pH. In this study, we analyzed multiple physiological responses of Bostrychia montagnei and Bostrychia calliptera from two biogeographic provinces of Brazil (Tropical Southwestern Atlantic [TSA] and Warm Temperate Southwestern Atlantic [WTSA]) after culturing them at a set of bioreactors in three pH levels (7.2, 7.6, and 8.0). Two pH were decreased by CO2 enrichment into the culture medium. Molecular analyses using plastidial (rbcL-3P) and mitochondrial (COI-5P) DNA markers were also performed to identify genetic divergences between macroalgae from TSA and WTSA. Molecular evidence of COI-5P marker demonstrated that the specimens of both B. montagnei and B. calliptera from TSA and WTSA constitute different haplotypes, with a strong segregation between them. Macroalgae from both localities increased their growth in treatments of decreased pH with increased CO2 availability. Overall, physiological responses of the algae were not negatively affected by decreased pH. B. montagnei from TSA increased its polysaccharide and allophycocyanin content at pH 7.2, and B. montagnei from WTSA increased its low molecular weight carbohydrate content at pH 7.2 as well. Antioxidant activity — a proxy for physiological stress — was not affected by decreased pH. Our study indicates that haplotypes of B. montagnei and B. calliptera from TSA and WTSA can be relevant to CO2 sequestration in mangroves once they are tolerant of decreased pH and increase their growth under increased CO2 availability.

Physiological role of isocitrate lyase in dibenzo-p-dioxin and dibenzofuran metabolism by Sphingomonas wittichii RW1

BackgroundSphingomonas wittichii RW1 is one out of three strains capable of metabolizing dioxin as a sole source for carbon and energy. Under laboratory conditions the degradation rates for these aromatics are relatively high (5 and 8 h for dibenzofuran (DBF) and dibenzo-p-dioxin (DD), respectively). However, their degradation rates are much lower in the environment due to several factors. One of these factors is the availability of other carbon sources. Acetate is a metabolized carbon source by S. wittichii RW1 and its presence in the environment would have a negative impact on DBF and DD degradation. In addition, expression of most of the genes for DBF and DD degradation were downregulated when grown on acetate compared to their growth on DBF and DD. We hypothesized that blocking the acetate utilization pathway in S. wittichii RW1 would prevent it from using acetate when present along with DD and DBF in contaminated sites. ResultsBlocking the glyoxylate shunt by deleting isocitrate lyase gene (icl) prevented the mutant strain (RW1Δicl) from using acetate as a sole carbon source thus depending on available DBF and DD in polluted sites. Our results showed that deletion of icl did not affect growth of S. wittichii RW1 on DBF and DD but blocked it from growing on acetate. ConclusionOur results introduces an engineered strain that can be used as a new candidate to clean dioxin-contaminated sites which are rich with acetate.

Carbon sources supporting macrobenthic crustaceans in tropical eastern pacific mangroves

In tropical mangroves, crustaceans are one of the most relevant components in terms of abundance, occurrence, biomass, function, and human welfare. Since these organisms are involved in the trophic dynamics of mangroves and also, are important fishery resources, the study of carbon used by crustaceans in mangrove ecosystems is important to understand the food web functioning of mangroves and estuaries, and how energy and matter flow through these organisms, via their participation in different trophic pathways. We compared the isotopic composition (δ13C/δ15N) of carbon sources and macrobenthic crustacean species of three macrotidal (fringe, internal and external riverine) mangroves, located in the central Colombian Pacific, and used a Bayesian aproached to evaluate if geomorphology induces differences in the isotopic composition and in the relative contribution of primary producers to different species of macrobenthic crustaceans. Differences were found in the isotopic composition between the three systems, with 13C values generally enriched for the external riverine mangrove, indicating a marine influence. The relative contribution of microphytobenthos with respect to other primary sources was highest in the three mangrove systems, followed by mangrove and seston in the internal and external riverine respectively, and macroalgae in fringe system. However, differences were found in the contribution of all sources depending on the species and type of mangrove but trophic pathways of the systems are the same. Our results confirm part of the hypothesis of this research, showing that geomorphological configuration of the habitat induces significative differences in the isotopic composition of primary sources and macrobenthic crustaceans but, the carbon utilization patterns of macrobenthic crustaceans show the same main trophic pathways (mangroves and microphytobenthos) in all three systems, due to the similar availability of carbon sources despite geomorphological differences.

The impact of Nitrogen and Carbon Sources on the Biofilm Formation of Micrococcus luteus

This study is conducted to show the influence of different media on the extent and pattern of biofilm formation. Trends of newly emerging pathogens continue steadily. Micrococcus luteus is one of those emerging pathogens. Incidental isolations of this bacteria have been recorded from patients with urinary tract infection and/or immunocompromised conditions. Biofilm formation on the surfaces of wound drainage and urinary catheters has been reported to be the source of recurrence and colonization of the pathogen in those patients. The current study's approach assesses the role of nutrient availability on the patterns of attachment till detachment and dispersion of the biofilms. Different species of bacteria are used to correlate their biofilm formation trend. Micrococcus luteus was chosen in the study due to its emerging pathogenic potential. Validation of biofilm formation is provided by involving Proteus mirabilis; which is an ideal biofilm producer, in parallel with Micrococcus luteus throughout the entire experimental settings. The findings of this study confirm statistically significant differences in biofilm formation patterns when nutritionally different culture media have been utilized to resemble possible environments for the pathogen. Micrococcus luteus has been found to possess the highest potential to produce biofilm in peptone water media where it over paced Proteus mirabilis. Results of the study reveal that both availability and scarcity of carbon and nitrogen sources can influence both positively and negatively on the patterns of biofilm formation by different strains of bacteria and incubation time. Biofilm assessment is an inevitable technique for nosocomial infections due to the complications of antibiotic susceptibility trends that prolong the hospitalization process, which limits treatment capacity.

Characterization of the biofilm structure and microbial diversity of sulfate-reducing bacteria from petroleum produced water supplemented by different carbon sources

Colonization by sulfate-reducing bacteria (SRB) in environments associated with oil is mainly dependent on the availability of sulfate and carbon sources. The formation of biofilms by SRB increases the corrosion of pipelines and oil storage tanks, representing great occupational and operational risks and respective economic losses for the oil industry. The aim of this study was to evaluate the influence of the addition of acetate, butyrate, lactate, propionate and oil on the structure of biofilm formed in carbon steel coupons, as well as on the diversity of total bacteria and SRB in the planktonic and sessile communities from petroleum produced water. The biofilm morphology, chemical composition, average roughness and the microbial diversity was analyzed. In all carbon sources, formation of dense biofilm without morphological and/or microbial density differences was detected, with the most of cells observed in the form of individual rods. The diversity and richness indices of bacterial species in the planktonic community was greater than in the biofilm. Geotoga was the most abundant genus, and more than 85% of SRB species were common to all treatments. The functional predicted profile shown that the observed genres in planktonic communities were related to the reduction of sulfate, sulfite, elementary sulfur and other sulfur compounds, but the abundance varied between treatments. For the biofilm, the functions predicted profile for the oil treatment was the one that most varied in relation to the control, while for the planktonic community, the addition of all carbon sources interfered in the predicted functional profile. Thus, although it does not cause changes in the structure and morphology biofilm, the supplementation of produced water with different carbon sources is associated with changes in the SRB taxonomic composition and functional profiles of the biofilm and the planktonic bacterial communities.

Rivers draining contrasting landscapes exhibit distinct potentials to emit diffusive methane (CH4)

Methane (CH4) is the second most important greenhouse gas, contributing approximately 17% of radiative forcing, and CH4 emissions from river networks due to intensified human activities have become a worldwide issue. However, there is a dearth of information on the CH4 emission potentials of different rivers, especially those draining contrasting watershed landscapes. Here, we examined the spatial variability of diffusive CH4 emissions and discerned the roles of environmental factors in influencing CH4 production in different river reaches (agricultural, urban, forested and mixed-landscape rivers) from the Chaohu Lake Basin in eastern China. According to our results, the urban rivers most frequently exhibited extremely high CH4 concentrations, with a mean concentration of 5.46 μmol L−1, equivalent to 4.1, 9.7, and 7.2 times those measured in the agricultural, forested, and mixed-landscape rivers, respectively. The availability of carbon sources and total phosphorus were commonly identified as the most important factors for CH4 production in agricultural and urban rivers. Dissolved oxygen and oxidation-reduction potential were separately discerned as important factors for the forested and mixed-landscape rivers, respectively. Monte Carlo flux estimations demonstrated that rivers draining contrasting landscapes exhibit distinct potentials to emit CH4. The urban rivers had the highest CH4 emissions, with a flux of 9.44 mmol m−2 d−1, which was 5.1–10.4 times higher than those of the other river reaches. Overall, our study highlighted that management actions should be specifically targeted at the river reaches with the highest emission potentials and should carefully consider the influences of different riverine environmental conditions as projected by their watershed landscapes.

Chlorella sp. Mg shows special trophic transitions and biomass production

Most microalgae have strategy to switch their growing modes depending on the availability of light and carbon sources. Unexpectedly mixotrophic Chlorella sp. Mg produced much less biomass than its heterotrophic counterpart. Investigation of the growth, photosynthetic activity, and ROS levels showed that mixotrophic Chlorella sp. Mg did not repress its photosynthesis activity upon glucose treatment, which accumulated much higher amounts of ROSs than heterotrophic one. Treatment of DCMU to the mixotrophic cells decreased photosynthetic activity and ROS levels, resulting in an increase of biomass by 62%. Decreased light intensity for the mixotrophic cells led to a similar result to that of DCMU treatment. Transcriptomic analysis showed that mixotrophic Chlorella sp. Mg did not up-regulate the hexokinase (HXK) and did not down-regulate most photosynthesis-related genes. Taken together, the algal HXK gene may not act as a glucose sensor, which could lead to unbalance of carbon metabolisms and low biomass production.

The HMGB Protein KlIxr1, a DNA Binding Regulator of Kluyveromyces lactis Gene Expression Involved in Oxidative Metabolism, Growth, and dNTP Synthesis.

In the traditional fermentative model yeast Saccharomyces cerevisiae, ScIxr1 is an HMGB (High Mobility Group box B) protein that has been considered as an important regulator of gene transcription in response to external changes like oxygen, carbon source, or nutrient availability. Kluyveromyces lactis is also a useful eukaryotic model, more similar to many human cells due to its respiratory metabolism. We cloned and functionally characterized by different methodologies KlIXR1, which encodes a protein with only 34.4% amino acid sequence similarity to ScIxr1. Our data indicate that both proteins share common functions, including their involvement in the response to hypoxia or oxidative stress induced by hydrogen peroxide or metal treatments, as well as in the control of key regulators for maintenance of the dNTP (deoxyribonucleotide triphosphate) pool and ribosome synthesis. KlIxr1 is able to bind specific regulatory DNA sequences in the promoter of its target genes, which are well conserved between S. cerevisiae and K. lactis. Oppositely, we found important differences between ScIrx1 and KlIxr1 affecting cellular responses to cisplatin or cycloheximide in these yeasts, which could be dependent on specific and non-conserved domains present in these two proteins.

Application of wheat flour (Triticum aestivum) on spore density and sporulation efficiency of Bacillus megaterium isolated from Litopenaeus vannamei gastrointestinal tract

Abstract. Mahariawan IMD, Kusuma WE, Yuniarti A, Beltran MAG, Hariati AM. 2021. Application of wheat flour (Triticum aestivum) on spore density and sporulation efficiency of Bacillus megaterium isolated from Litopenaeus vannamei gastrointestinal tract. Biodiversitas 22: 3709-3715. Bacillus megaterium is frequently used in fish farming, such as white shrimp (Litopenaeus vannamei) pond, which can produce spores with high stability in its implementation. Currently, spore production still requires the availability of high-cost carbon sources. The objective of this research was to evaluate the effect of different wheat flour doses on spore density and sporulation efficiency of B. megaterium BM1. In flasks, 50 mL of each test medium was treated with different doses of wheat (10, 20, 30 and 40 g. L-1, respectively) and glucose was used as a control. Each treatment was inoculated with B. megaterium BM1 (2.6 x 108 CFU. mL-1) and incubated in a shaker incubator (120 rpm) at 37 °C for 120 hours. The results showed that the highest vegetative cell concentration (17 x 108 CFU. mL-1), growth rate (0.8 hour-1) and spore (14.7 x 108 spores. mL-1) were found in the wheat flour dose of 30 g. L-1. Furthermore, the highest sporulation efficiency was achieved at 20 g. L-1 of wheat (91.30%) and germination should be done at a dose less than 40 g. L-1. The size of the spores was 1.35-1.39 µm. Thus, 30 g. L-1 of wheat flour is a potential dose to produce spore for probiotic candidates.

Assessment of Carbon Substrate Catabolism Pattern and Functional Metabolic Pathway for Microbiota of Limestone Caves.

Carbon utilization of bacterial communities is a key factor of the biomineralization process in limestone-rich curst areas. An efficient carbon catabolism of the microbial community is associated with the availability of carbon sources in such an ecological niche. As cave environments promote oligotrophic (carbon source stress) situations, the present study investigated the variations of different carbon substrate utilization patterns of soil and rock microbial communities between outside and inside cave environments in limestone-rich crust topography by Biolog EcoPlate™ assay and categorized their taxonomical structure and predicted functional metabolic pathways based on 16S rRNA amplicon sequencing. Community level physiological profiling (CLPP) analysis by Biolog EcoPlate™ assay revealed that microbes from outside of the cave were metabolically active and had higher carbon source utilization rate than the microbial community inside the cave. 16S rRNA amplicon sequence analysis demonstrated, among eight predominant bacterial phylum Planctomycetes, Proteobacteria, Cyanobacteria, and Nitrospirae were predominantly associated with outside-cave samples, whereas Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes were associated with inside-cave samples. Functional prediction showed bacterial communities both inside and outside of the cave were functionally involved in the metabolism of carbohydrates, amino acids, lipids, xenobiotic compounds, energy metabolism, and environmental information processing. However, the amino acid and carbohydrate metabolic pathways were predominantly linked to the outside-cave samples, while xenobiotic compounds, lipids, other amino acids, and energy metabolism were associated with inside-cave samples. Overall, a positive correlation was observed between Biolog EcoPlate™ assay carbon utilization and the abundance of functional metabolic pathways in this study.

Adaptability of a Caproate-Producing Bacterium Contributes to Its Dominance in an Anaerobic Fermentation System.

The transformation of diverse feedstocks into medium-chain fatty acids (MCFAs) by mixed cultures is a promising biorefinery route because of the high value of MCFAs. A particular concern is how to maintain the microbial consortia in mixed cultures to achieve stable MCFA production. The Chinese strong aroma-type liquor (Baijiu) fermentation system continually produces caproic acid for decades through a spontaneous inoculation of anaerobes from pit mud into fermented grains. Therefore, illuminating the dominant caproate-producing bacterium (CPB) in pit mud and how the CPB is sustained in the spontaneous fermentation system will help to reveal the microbiological mechanisms of stable caproate production. Here, we examined pit mud samples across four Chinese strong aroma-type Baijiu-producing areas and found that a caproate-producing Caproicibacterium sp. was widely distributed in these distilleries, with relative abundance ranging from 1.4 to 35.5% and an average abundance of 11.4%. Through controlling carbon source availability, we obtained different simplified caproate-producing consortia and found that the growth advantage of Caproicibacterium sp. was highly dependent on glucose. Then, two strains, named Caproicibacterium sp. strain LBM19010 and Caproicibacterium sp. strain JNU-WLY1368, were isolated from pit mud of two regions. The metabolic versatility of this species utilizing starch, maltose, glucose, and lactate reflected its adaptability to the fermentation environment where these carbon sources coexist. The simultaneous utilization of glucose and lactate contributed to the balance between cell growth and pH homeostasis. This study reveals that multiple adaptation strategies employed by the predominant CPB promotes its stability and dominance in a saccharide- and lactate-rich anaerobic habitat. IMPORTANCE The Chinese strong aroma-type liquor (Baijiu) fermentation environment is a typical medium-chain fatty acid-producing system with complex nutrients. Although several studies have revealed the correlation between microbial community composition and abiotic factors, the adaptation mechanisms of dominant species to abiotic environment are still unknown in this special anaerobic habitat. This study identified the predominant CPB in Chinese strong aroma-type Baijiu fermentation system. Metabolic versatility and flexibility of the dominant CPB with a small-size genome indicated that this bacterium can effectively exploit available carbon and nitrogen sources, which could be a key factor to promote its ecological success in a multispecies environment. The understanding of growth and metabolic features of the CPB responsible for its dominance in microbial community will not only contribute to the improvement of Chinese strong aroma-type Baijiu production but also expand its potential industrial applications in caproate production.

An AMP-activated protein kinase complex with two distinctive alpha subunits is involved in nutritional stress responses in Trypanosoma cruzi.

Trypanosoma cruzi, the etiological agent of Chagas disease, has a digenetic life cycle. In its passage from the insect vector to the mammalian host, and vice versa, it must be prepared to cope with abrupt changes in environmental conditions, such as carbon source, pH, temperature and osmolarity, in order to survive. Sensing and signaling pathways that allow the parasite to adapt, have unique characteristics with respect to their hosts and other free-living organisms. Many of the canonical proteins involved in these transduction pathways have not yet been found in the genomes of these parasites because they present divergences either at the functional, structural and/or protein sequence level. All of this makes these pathways promising targets for therapeutic drugs. The AMP-activated protein kinase (AMPK) is a serine/threonine kinase activated by environmental stresses such as osmotic stress, hypoxia, ischaemia and exercise that results in reduction of ATP and increase of AMP levels. Thus, AMPK is regarded as a fuel gauge, functioning both as a nutrient and an energy sensor, to maintain energy homeostasis and, eventually, to protect cells from death by nutrient starvation. In the present study we report the characterization of AMPK complexes for the first time in T. cruzi and propose the function of TcAMPK as a novel regulator of nutritional stress in epimastigote forms. We show that there is phosphotransferase activity specific for SAMS peptide in epimastigotes extracts, which is inhibited by Compound C and is modulated by carbon source availability. In addition, TcAMPKα2 subunit has an unprecedented functional substitution (Ser x Thr) at the activation loop and its overexpression in epimastigotes led to higher autophagic activity during prolonged nutritional stress. Moreover, the over-expression of the catalytic subunits resulted in antagonistic phenotypes associated with proliferation. Together, these results point to a role of TcAMPK in autophagy and nutrient sensing, key processes for the survival of trypanosomatids and for its life cycle progression.

Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

Diauxie, or the sequential consumption of carbohydrates in bacteria such as Escherichia coli, has been hypothesized to be an evolutionary strategy which allows the organism to maximize its instantaneous specific growth-giving the bacterium a competitive advantage. Currently, the computational techniques used in industrial biotechnology fall short of explaining the intracellular dynamics underlying diauxic behavior. In particular, the understanding of the proteome dynamics in diauxie can be improved. We developed a robust iterative dynamic method based on expression- and thermodynamically enabled flux models to simulate the kinetic evolution of carbohydrate consumption and cellular growth. With minimal modeling assumptions, we couple kinetic uptakes, gene expression, and metabolic networks, at the genome scale, to produce dynamic simulations of cell cultures. The method successfully predicts the preferential uptake of glucose over lactose in E. coli cultures grown on a mixture of carbohydrates, a manifestation of diauxie. The simulated cellular states also show the reprogramming in the content of the proteome in response to fluctuations in the availability of carbon sources, and it captures the associated time lag during the diauxie phenotype. Our models suggest that the diauxic behavior of cells is the result of the evolutionary objective of maximization of the specific growth of the cell. We propose that genetic regulatory networks, such as the lac operon in E. coli, are the biological implementation of a robust control system to ensure optimal growth.

Modulation of green to red photoconversion of GFP during fluorescent microscopy by carbon source and oxygen availability.

Studies have reported on the ability of green fluorescent proteins to photoconvert into a red fluorescent form under various conditions, such as the presence of oxidants, hypoxia, as well as under benign conditions using irradiation with a 405 nm laser. Here, we show that in Saccharomyces cerevisiae yeast green fluorescent protein (GFP) (S65T) fused to different cellular proteins can easily photoconvert into a red form when cells are grown in media with nonfermentable carbon sources. This photoconversion occurs during standard microscopy between glass slide and coverslip but is completely prevented by imaging on pads of solid medium or in a large volume of medium on an inverted microscope. The observed effect was due to rapid hypoxia of cells with respiratory metabolism in standard conditions for upright microscopy. Photoconversion could be prevented by antioxidant treatment, suggesting that it proceeds via the effects of reactive oxidative species emerging in response to oxygen deficiency. Our results show the need for caution during upright microscopy imaging in conditions where there is active respiration and demonstrate simple approaches to prevent unwanted GFP photoconversion. They also provide easy means of performing photoconversion experiments on existing GFP-bearing cell lines, at least in the case of yeast.

Reliance of deep-sea benthic macrofauna on ice-derived organic matter highlighted by multiple trophic markers during spring in Baffin Bay, Canadian Arctic

Benthic organisms depend primarily on seasonal pulses of organic matter from primary producers. In the Arctic, declines in sea ice due to warming climate could lead to changes in this food supply with as yet unknown effects on benthic trophic dynamics. Benthic consumer diets and food web structure were studied in a seasonally ice-covered region of Baffin Bay during spring 2016 at stations ranging in depth from 199 to 2,111 m. We used a novel combination of highly branched isoprenoid (HBI) lipid biomarkers and stable isotope ratios (δ13C, δ15N) to better understand the relationship between the availability of carbon sources in spring on the seafloor and their assimilation and transfer within the benthic food web. Organic carbon from sea ice (sympagic carbon [SC]) was an important food source for benthic consumers. The lipid biomarker analyses revealed a high relative contribution of SC in sediments (mean SC% ± standard deviation [SD] = 86% ± 16.0, n = 17) and in benthic consumer tissues (mean SC% ± SD = 78% ± 19.7, n = 159). We also detected an effect of sea-ice concentration on the relative contribution of SC in sediment and in benthic consumers. Cluster analysis separated the study region into three different zones according to the relative proportions of SC assimilated by benthic macrofauna. We observed variation of the benthic food web between zones, with increases in the width of the ecological niche in zones with less sea-ice concentration, indicating greater diversity of carbon sources assimilated by consumers. In zones with greater sea-ice concentration, the higher availability of SC increased the ecological role that primary consumers play in driving a stronger transfer of nutrients to higher trophic levels. Based on our results, SC is an important energy source for Arctic deep-sea benthos in Baffin Bay, such that changes in spring sea-ice phenology could alter benthic food-web structure.

Two-stage mineral dissolution and precipitation related to organic matter degradation: Insights from in situ C–O isotopes of zoned carbonate cements

Mineral dissolution and precipitation, particularly of carbonate minerals, are ubiquitous and significant diagenetic processes in sedimentary rocks. However, the impacts of organic matter degradation on these processes in single systems remain unclear because the timing and fluid sources during progressive burial are poorly constrained. To address this issue, in situ C–O isotope analyses were conducted for zoned dolomite–ankerite/calcite cements from the Permian Lucaogou Formation in the Junggar Basin, China, using secondary ion mass spectrometry (SIMS) combined with mineralogical and elemental analyses. Carbonate minerals can be divided into early-stage and late-stage precipitations based on distinct variations in δ18O (−18.3 to −0.7‰ V-PDB), δ13C (−3.6 to +20.8‰ V-PDB), and Fe content (Fe# ranging from 0.002 to 0.373). The chemo-isotopically zoned carbonate cements record the thermal and chemical conditions of pore fluids during the burial process. The difference in δ18O values between the early and late precipitation (i.e., Δ18O [early–late]) of 11.9‰, and the difference in δ13C values (i.e., Δ13C [early–late]) of 11.7‰, reveal significant changes in precipitation temperatures and the availability of carbon sources, respectively. Early-stage precipitation occurred in association with microbial methanogenesis at lower temperatures (~25 °C) during shallow burial (~300 m), whereas late-stage precipitation was related to thermally-induced decarboxylation at higher temperatures (~90 °C or ~110 °C) during deep burial (~2500 m or ~3200 m). These two stages of dissolved pore-filling precipitation correspond to two major periods of dissolution (i.e., eogenetic and mesogenetic dissolution). Diagenetic fluids, mainly CO2 and/or organic acids, were derived from the biological and thermal degradation of organic matter, respectively. These results constrain the isotopic responses of carbonates to organic matter degradation with increasing burial depth and provide significant insights into carbonate diagenesis in organic-rich sedimentary sequences.

Removal of sulfamethoxazole and tetracycline in constructed wetlands integrated with microbial fuel cells influenced by influent and operational conditions.

Constructed wetlands integrated with microbial fuel cells (MFC-CWs) have been recently developed and tested for removing antibiotics. However, the effects of carbon source availability, electron transfer flux and cathode conditions on antibiotics removal in MFC-CWs through co-metabolism remained unclear. In this study, four experiments were conducted in MFC-CW microcosms to investigate the influence of carbon source species and concentrations, external resistance and aeration duration on sulfamethoxazole (SMX) and tetracycline (TC) removal and bioelectricity generation performance. MFC-CWs supplied with glucose as carbon source outperformed other carbon sources, and moderate influent glucose concentration (200mgL-1) resulted in the best removal of both SMX and TC. Highest removal percentages of SMX (99.4%) and TC (97.8%) were obtained in MFC-CWs with the external resistance of 700Ω compared to other external resistance treatments. SMX and TC removal percentages in MFC-CWs were improved by 4.98% and 4.34%, respectively, by increasing the aeration duration to 12h compared to no aeration. For bioelectricity generation performance, glucose outperformed sodium acetate, sucrose and starch, with the highest voltages of 386±20mV, maximum power density (MPD) of 123.43mWm-3, and coulombic efficiency (CE) of 0.273%. Increasing carbon source concentrations from 100 to 400mgL-1, significantly (p<0.05) increased the voltage and MPD, but decreased the internal resistance and CE. The highest MPD was obtained when the external resistance (700Ω) was close to the internal resistance (600.11Ω). Aeration not only improved the voltage and MPD, but also reduced the internal resistance. This study demonstrates that carbon source species and concentrations, external resistances and aeration duration, all play vital roles in regulating SMX and TC removal in MFC-CWs.

The Inorganic Nutrient Regime and the mre Genes Regulate Cell and Filament Size and Morphology in the Phototrophic Multicellular Bacterium Anabaena.

The model cyanobacterium Anabaena sp. PCC 7120 exhibits a phototrophic metabolism relying on oxygenic photosynthesis and a complex morphology. The organismic unit is a filament of communicated cells that may include cells specialized in different nutritional tasks, thus representing a paradigm of multicellular bacteria. In Anabaena, the inorganic carbon and nitrogen regime influenced not only growth, but also cell size, cell shape, and filament length, which also varied through the growth cycle. When using combined nitrogen, especially with abundant carbon, cells enlarged and elongated during active growth. When fixing N2, which imposed lower growth rates, shorter and smaller cells were maintained. In Anabaena, gene homologs to mreB, mreC, and mreD form an operon that was expressed at higher levels during the phase of fastest growth. In an ntcA mutant, mre transcript levels were higher than in the wild type and, consistently, cells were longer. Negative regulation by NtcA can explain that Anabaena cells were longer in the presence of combined nitrogen than in diazotrophic cultures, in which the levels of NtcA are higher. mreB, mreC, and mreD mutants could grow with combined nitrogen, but only the latter mutant could grow diazotrophically. Cells were always larger and shorter than wild-type cells, and their orientation in the filament was inverted. Consistent with increased peptidoglycan width and incorporation in the intercellular septa, filaments were longer in the mutants, suggesting a role for MreB, MreC, and MreD in the construction of septal peptidoglycan that could affect intercellular communication required for diazotrophic growth.IMPORTANCE Most studies on the determination of bacterial cell morphology have been conducted in heterotrophic organisms. Here, we present a study of how the availability of inorganic nitrogen and carbon sources influence cell size and morphology in the context of a phototrophic metabolism, as found in the multicellular cyanobacterium Anabaena In Anabaena, the expression of the MreB, MreC, and MreD proteins, which influence cell size and length, are regulated by NtcA, a transcription factor that globally coordinates cellular responses to the C-to-N balance of the cells. Moreover, MreB, MreC, and MreD also influence septal peptidoglycan construction, thus affecting filament length and, possibly, intercellular molecular exchange that is required for diazotrophic growth. Thus, here we identified new roles for Mre proteins in relation to the phototrophic and multicellular character of a cyanobacterium, Anabaena.