The legacy of forest logging on organic matter inputs and storage in tropical streams

Riparian forests play an important role in stream ecosystems, as they support biodiversity, reduce water erosion, and provide litter that fuels aquatic biota. However, they are affected by great array of anthropogenic threats (e.g., fire, logging, and organic pollution), which alter species composition and their physical structure. Although forest recovery after disturbance such as logging can take decades, the legacy of forest clear-cut logging on key processes in tropical riparian ecosystems is mostly unknown. Here, we investigated how litter inputs (leaves, twigs, and reproductive parts) and storage, key processes for carbon and nutrient recycling and for forest and stream biota, are influenced by riparian vegetation undergoing succession (after 28 years from logging) through the comparison of reference and logged forest sites in the Cerrado biome. Litterfall was overall similar between forest types, but litterfall of twigs was twofold higher at logged than reference sites. Similarly, litter inputs from the bank to the stream (i.e., lateral inputs) and streambed storage were 50–60% higher at logged than reference sites. The higher litterfall observed in logged forests could be related to higher proportion of tree species that are characteristic of primary and secondary successional stages, including fast-growing and liana species, which often are more productive and common in anthropogenic areas. Our results showed that the legacy impact of clear-cut logging, even if residual woody vegetation is maintained in riparian buffers, can shift the type, quantity, and seasonality of litter subsidies to tropical streams. This knowledge should be considered within the context of management and conservation of communities and ecosystem processes in the forest-stream interfaces.     

A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis

Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 contigs (614 Mb) combining long- and short-read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC-FISH. Whole genome resequencing of six males and six females enabled the identification of 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) consistent with an XX/XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. The fshr gene displayed differential expression between male and female gonads from 86 days post-fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of amh and cyp19a1a, testis and ovary marker genes, respectively, in males and females. The Y-linked fshr allele, which included 24 nonsynonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X-linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.     

The effect of charcoal production on carbon cycling in African biomes

Using biomass for charcoal production in sub-Saharan Africa (SSA) may change carbon stock dynamics and lead to irreversible changes in the carbon balance, yet we have little understanding of whether these dynamics vary by biome in this region. Currently, charcoal production contributes up to 7% of yearly deforestation in tropical regions, with carbon emissions corresponding to 71.2 million tonnes of CO₂ and 1.3 million tonnes of CH₄. With a projected increased demand for charcoal in the coming decades, even low harvest rates may throw the carbon budget off-balance due to legacy effects. Here, we parameterized the dynamic global vegetation model LPJ-GUESS for six SSA biomes and examined the effect of charcoal production on net ecosystem exchange (NEE), carbon stock sizes and recovery time for tropical rain forest, montane forest, moist savanna, dry savanna, temperate grassland and semi-desert. Under historical charcoal regimes, tropical rain forests and montane forests transitioned from net carbon sinks to net sources, that is, mean cumulative NEE from −3.56 ± 2.59 kg C/m² to 2.46 ± 3.43 kg C/m² and −2.73 ± 2.80 kg C/m² to 1.87 ± 4.94 kg C/m² respectively. Varying charcoal production intensities resulted in tropical rain forests showing at least two times higher carbon losses than the other biomes. Biome recovery time varied by carbon stock, with tropical and montane forests taking about 10 times longer than the fast recovery observed for semi-desert and temperate grasslands. Our findings show that high biomass biomes are disproportionately affected by biomass harvesting for charcoal, and even low harvesting rates strongly affect vegetation and litter carbon and their contribution to the carbon budget. Therefore, the prolonged biome recoveries imply that current charcoal production practices in SSA are not sustainable, especially in tropical rain forests and montane forests, where we observe longer recovery for vegetation and litter carbon stocks.     

Root traits of perennial C4 grasses contribute to cultivar variations in soil chemistry and species patterns in particulate and mineral-associated carbon pool formation

Recent studies have indicated that the C₄ perennial bioenergy crops switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii) accumulate significant amounts of soil carbon (C) owing to their extensive root systems. Soil C accumulation is likely driven by inter- and intraspecific variability in plant traits, but the mechanisms that underpin this variability remain unresolved. In this study we evaluated how inter- and intraspecific variation in root traits of cultivars from switchgrass (Cave-in-Rock, Kanlow, Southlow) and big bluestem (Bonanza, Southlow, Suther) affected the associations of soil C accumulation across soil fractions using stable isotope techniques. Our experimental field site was established in June 2008 at Fermilab in Batavia, IL. In 2018, soil cores were collected (30 cm depth) from all cultivars. We measured root biomass, root diameter, specific root length, bulk soil C, C associated with coarse particulate organic matter (CPOM) and fine particulate organic matter plus silt- and clay-sized fractions, and characterized organic matter chemical class composition in soil using high-resolution Fourier-transform ion cyclotron resonance mass spectrometry. C₄ species were established on soils that supported C₃ grassland for 36 years before planting, which allowed us to use differences in the natural abundance of stable C isotopes to quantify C₄ plant-derived C. We found that big bluestem had 36.9% higher C₄ plant-derived C compared to switchgrass in the CPOM fraction in the 0–10 cm depth, while switchgrass had 60.7% higher C₄ plant-derived C compared to big bluestem in the clay fraction in the 10–20 cm depth. Our findings suggest that the large root system in big bluestem helps increase POM-C formation quickly, while switchgrass root structure and chemistry build a mineral-bound clay C pool through time. Thus, both species and cultivar selection can help improve bioenergy management to maximize soil carbon gains and lower CO₂ emissions.     

Light, temperature and nutrients as factors in photosynthetic adjustment to an elevated concentration of carbon dioxide

The short-term stimulation of the net rate of carbon dioxide exchange of leaves by elevated concentrations of CO₂ usually observed in C₃ plants sometimes does not persist. Experiments were conducted to test whether the patterns of response to the environment during growth were consistent with the hypotheses that photosynthetic adjustment to elevated CO₂ concentration is due to (1) feedback inhibition or (2) nutrient stress. Soybean [Glycine max (L.) Merr. cv. Williams] and sugar beet (Best vulgaris L. cv. Mono Hye-4) were grown from seed at 350 and 700 μl^? CO₂, at 20 and 25°C, at a photon flux density of 0.5 and 1.0 mmol m^?2 S^?1 and with three nutrient regimes until the third trifoliolate leaf of soybean or the sixth leaf of sugar beet had finished expanding. Net rates of CO₂ exchange of the most recently expanded leaves were then measured at both 350 and 700 μl 1^?1 CO₂. Plants grown at the elevated CO₂ concentration had net rates of leaf CO₂ exchange which were reduced by 33% in sugar beet and 23% in soybean when measured at 350 μl 1^?1 CO₂ and when averaged over all treatments. Negative photosynthetic adjustment to elevated CO₂ concentration was not greater at 20 than at 25°C, was not greater at a photon flux density of 1.0 than at 0.5 mmol m^?2 S^?1 and was not greater with limiting nutrients. Furthermore, in soybean, negative photosynthetic adjustment could be induced by a single night at elevated CO₂ concentration, with net rates of CO₂ exchange the next day equal to those of leaves of plants grown from seed at the elevated concentration of CO₂. These patterns do not support either the feedback-inhibition or the nutrient-stress hypothesis of photosynthetic adjustment to elevated concentrations of CO₂.     

EFFECTS OF VARIATION IN TEMPERATURE. I. ON THE BIOCHEMICAL COMPOSITION OF EIGHT SPECIES OF MARINE PHYTOPLANKTON1

The influence of temperature on the biochemical composition of eight species of marine phytoplankton was investigated. Thalassiosira pseudonana Hasle and Heim-dal, Phaeodactylum tricornutum Bohlin and, Pavlova lutheri Droop (three of eight species studied) had minimum values of carbon and nitrogen quotas at intermediate temperatures resulting in a broad U-shaped response in quotas over the temperature range of 10 to 25°C. Protein per cell also had minimum values at intermediate temperatures for six species. For T. pseudonana, P. tricornutum, and P. lutheri, patterns of variation in carbon, nitrogen, and protein quotas as a function of temperature were similar. Over all species, lipid and carbohydrate per cell showed no consistent trends with temperature. Only chlorophyll a quotas and the carbon: chlorophyll a ratios (θ) showed consistent trends across all species. Chlorophyll a quotas were always lower at 10°C than at 25°C. Carbon: chlorophyll a ratios (θ) were always higher at 10°C than at 25°C. We suggest that although θ consistently increases at lower temperatures, the relationship between temperature and θ ranges from linear to exponential and is species specific. Accordingly, the interspecific variance in θ that results from species showing a range of possible responses to temperature increases as temperature declines and reaches a maximum at low temperatures. High photon flux densities appear to increase the potential interspecific variance in the carbon: chlorophyll a ratio and therefore exacerbate these trends.     

VARIABILITY IN NITRATE UPTAKE KINETICS IN THALASSIOSIRA PSEUDONANA (BACILLARIOPHYCEAE)1

Short-term (1–9 min) nitrate uptake kinetics were measured in Thalassiosira pseudonana (Hust.) Hasle & Heimdal grown in nitrate-limited, ammonium-limited, and nitrate-sufficient continuous cultures. For all cultures, maximal nitrate uptake rates did not develop until approximately 3 min after nitrate addition; thereafter, nitrate uptake rates remained constant or declined slightly. The K_s and V_max for the nitrate-limited cultures were higher at any growth rate than those for the ammonium-limited or nitrate-sufficient cultures. Thus, much higher nitrate concentrations would be required to saturate nitrate uptake in nitrate-limited Thalassiosira pseudonana than is usually considered necessary. The lack of data for other species grown under a range of environmental conditions makes it difficult to generalize about the effect of preconditioning on nitrate uptake kinetics.     

INORGANIC CARBON LIMITATION OF PHOTOSYNTHESIS IN ULVA ROTUNDATA (CHLOROPHYTA)1

A computerized oxygen electrode Astern was used to make rapid and accurate measurements of photosynthetic light and dissolved inorganic carbon (DIC) response cures with a macroalga. Ulva rotundata Blid. was grown in an outdoor, continuous flow system in seawater under sunlight or 9% of sunlight at Beaufort, North Carolina. The light compensation points in the shade- and sun-grown plants, measured in seawater, were at photon flux densities (PFDs) of 16 and 27 μmol. Photons·m^?2·s^?1, respectively but the quantum yield of O₂ evolution was not significantly different. Rates of photosynthesis in seawater per unit area of thallus under saturating light and rates of dark respiration were about 1.5-fold higher in sun- than in shade-grown plants. The concentration of DIC in seawater (approximately 2 mM) limited photosynthesis at absorbed PFDs above 60–70 μmol photons·m^?2·s^?1 Addition of 20 mM inorganic carbon had no effect on quantum yield but caused about a 1.5-fold increase in the light-saturated photosynthetic rate in both shade- and sun-grown Ulva. The effect of DIC supplementation was greatest in plants grown in October and least in plants grown in June. The light- and DIC-saturated rate of photosynthesis in seawater was similar to the maximum rate obtained by exposing Ulva to 10% CO₂, in the gas phase. The carbon isotope values (δ¹³C, reflecting the ¹³C/¹²C ratio compared to a standard) of Ulva grown in the same seawater supply were dependent on light and agitation. Samples from Beaufort Inlet were more negative (δ¹³C value, ?20.03‰) than those grown in bright light with agitation (δ¹³C value, ?17.78‰ outdoors; ?17.23‰ indoors), which may indicate DIC supply limited carbon uptake in seawater.     

CHANGES IN CELL CHEMICAL COMPOSITION DURING THE LIFE CYCLE OF SCRIPPSIELLA TROCHOIDEA (DINOPHYCEAE)1

The cellular content of carbon, nitrogen, amino acids, polysaccharides, phosphorus and adenosine trtphosphate (ATP) was determined at several stages during the life cycle of the dinoflagellate Scrippsiella trochoidea (Stein) Loeblich. Carbon per cell decreased slightly between exponential and stationary phase growth in vegetative cells whereas nitrogen per cell did not change. Both of these cellular components increased markedly on encystment and then decreased to vegetative cell levels during dormancy and germination. C/N ratios increased gradually during cyst dormancy and activation, reflecting a more rapid decrease in N than in C pools, even though both decreased through time. Amino acid composition was relatively constant during the vegetative cell stages; glutamic acid was the dominant component. Arginine was notably higher in cysts than in vegetative cells but decreased significantly during germination, suggesting a role in nitrogen storage. The ratio of neutral ammo acids to total ammo acids (NAA/TAA) decreased as cysts were formed and then gradually increased during storage and germination. The ratio of basic ammo acids to total ammo acids (BAA/TAA) changed in the opposite direction of NAA/TAA, whereas the ratio of acidic acids to total amino adds (AAA/TAA) was generally invariant. Ammo acid pools were not static during the resting slate in the cysts: there was degradation or biosynthesis of certain, but not all, classes of these compounds. The monosacchande composition of cold and hot water extracted polysaccharides was quite different between cells and cysts. A high percentage of glucose in cysts suggests that the storage carbohydrate is probably in the form of glucan. Total cellular phosphorus was higher in all cyst stages than in vegetative cells. However, ATP-cell^?1 decreased as vegetative cells entered stationary phase and encysted, and continued to decrease in cysts during dark cold storage. ATP increased only as the cysts were activated at warm temperatures in the light and began to germinate. The above data demonstrate that dormancy and quiescence are not periods of inactive metabolism but instead are times when numerous biochemical transformations are occurring that permit prolonged survival in a resting state.     

CARBON FIXATION IN CULTURED MARINE BENTHIC DIATOMS1

The enzyme activity of ribulose 1, 5-bisphosphate carboxylase-oxygenase (RuBisCO) and phosphoenolpyruvate carboxylase (PEPC) was measured in four species of marine benthic diatoms isolated from subtidal sediments of Graveline Bayou, Mississippi. Enzyme activities were measured in cultures of Amphora micrometra Giffen, A. tenerrima Aleem and Hustedt, Nitzschia fontifuga Cholnoky, and Nitzschia vermicularis Grunow that were grown at light levels supporting μ_max and at light-limiting irradiances. All four species exhibited similar RuBisCO: PEP ratios (range = 1–1.8) at μ_max the lowest ratio (0.4) was observed in A. micrometra. Reduced light levels increased PEPC relative to that measured at μ_max in two species. Two-dimensional paper chromatography was used to determine the first products of carbon fixation in A. micrometra After a 15 s incorporation period, the first product of photosynthetic carbon fixation was 3-phosphoglycerate even though this alga had a PEPC activity that was three times higher than that of RuBisCO. After 30 s, over 50% of the recovered radioactivity was still in this compound. Stable carbon isotope analyses of a mixture of the four pennate diatoms also suggest the predominant carbon fixation pathway in these benthic diatoms was similar to C3 plants.