Oxygen effects on methane production and oxidation in humid tropical forest soils

We investigated the effects of oxygen (O₂) concentration on methane (CH₄) production and oxidation in two humid tropical forests that differ in long‐term, time‐averaged soil O₂ concentrations. We identified sources and sinks of CH₄ through the analysis of soil gas concentrations, surface emissions, and carbon isotope measurements. Isotope mass balance models were used to calculate the fraction of CH₄ oxidized in situ. Complementary laboratory experiments were conducted to determine the effects of O₂ concentration on gross and net rates of methanogenesis. Field and laboratory experiments indicated that high levels of CH₄ production occurred in soils that contained between 9±1.1% and 19±0.2% O₂. For example, we observed CH₄ concentrations in excess of 3% in soils with 9±1.1% O₂. CH₄ emissions from the lower O₂ sites were high (22–101 nmol CH₄ m^?2 s^?1), and were equal in magnitude to CH₄ emissions from natural wetlands. During peak periods of CH₄ efflux, carbon dioxide (CO₂) emissions became enriched in ¹³C because of high methanogenic activity. Gross CH₄ production was probably greater than flux measurements indicated, as isotope mass balance calculations suggested that 48–78% of the CH₄ produced was oxidized prior to atmospheric egress. O₂ availability influenced CH₄ oxidation more strongly than methanogenesis. Gross CH₄ production was relatively insensitive to O₂ concentrations in laboratory experiments. In contrast, methanotrophic bacteria oxidized a greater fraction of total CH₄ production with increasing O₂ concentration, shifting the δ¹³C composition of CH₄ to values that were more positive. Isotopic measurements suggested that CO₂ was an important source of carbon for methanogenesis in humid forests. The δ¹³C value of methanogenesis was between ?84‰ and ?98‰, which is well within the range of CH₄ produced from CO₂ reduction, and considerably more depleted in ¹³C than CH₄ formed from acetate.     

The influence of glucose and other sources of carbon on nitrate reduction rates in two temperate forest soils

The effects of different sources of organic carbon on the potential NO ₃ ⁻ reduction rates in an acid mull and an anmoor (anmoor is a type of soil which is rich in organic matter, remains water saturated most of the time and where organic and mineral fractions are closely associated) were studied under anaerobic incubation. The disappearance of NO ₃ ⁻ was higher in the anmoor than in the mull in all cases. This contradicts our previous findings where the apparent denitrification was higher in the mull than in the anmoor in the presence of added glucose. This seems to indicate that drying of soil samples might have caused the formation of stable soil aggregates in the case of anmoor (containing 16% of organic matter). Thus a favourable condition was created for securing improved diffusion of nutrients in the anmoor. Glucose, a readily available source of carbon, led to a very high degree of NO ₃ ⁻ disappearance. Among other sources, the cellulose caused higher reduction of NO ₃ ⁻ than litter and lignin. The accumulation although small, of NH ₄ ⁺ which was presumably formed (at least partially) during dissimilatory reduction of NO ₃ ⁻ , and its biological immobilization were more apparent in the anmoor than in the mull.     

Storms can cause Europe-wide reduction in forest carbon sink

Disturbance of ecosystems is a major factor in regional carbon budgets, and it is believed to be partly responsible for the large inter-annual variability of the terrestrial part of the carbon balance. Forest fires have so far been considered as the most important disturbance but also other forms of disturbance such as insect outbreaks or wind-throw might contribute significantly to the largely unexplained inter-annual variability, at least in specific regions. The effect of wind-throw has not yet been estimated because of lack of data on how carbon fluxes are affected. The Gudrun storm, which hit Sweden in January 2005, resulted in ca. 66 million m³ of wind-thrown stem wood on an area of ca. 272 000 ha. Using a model (BIOME-BGC) calibrated to CO₂ flux measurements at two sites, the annual net ecosystem productivity during the first year after the storm was estimated to be in the range −897 to −1259 g C m⁻² yr⁻¹. This is a much higher loss compared with harvested (clear-cut) forests in Europe, which ranged between ca. −420 and −100 g m⁻² yr⁻¹. The reduction in the carbon sink scaled to the whole wind-thrown area was estimated at ca. 3 million tons C during the first year. By historical data on wind-throw in Europe combined with modelling, we estimated that the large Lothar storm in 1999 reduced the European carbon balance by ca. 16 million tons C, this is ca. 30% of the net biome production in Europe. We conclude that the impact of increased forest damage by more frequent storms in future climate change scenarios must be considered and that intermittent large wind-throw events may explain a part of the large inter-annual variability in the terrestrial carbon sink.     

Seasonal rate of nitrate reduction in two temperate forest soils

Rainfall and throughfall chemistry beneath Sitka spruce of four ages were determined for a one year period. Throughfall beneath the older stands was consistently much more acid than rainfall. The H-ion flux was more than twice that in rainfall. Throughfall beneath the younger stands was only slightly more acid than rainfall, but the throughfall H-ion flux was considerbly less than in rainfall because the canopy intercepted a large proportion of rainfall. Concentrations and fluxes of other major cations and anions were greater in throughfall than precipitation for all crop ages.     

农田和森林土壤中氧化亚氮的产生与还原

采用土壤淤浆方法对丹麦农田和山毛榉森林土壤反硝化过程中Ｎ２Ｏ的产生与还原进行了研究。同时考察了硝酸根和铵离子对反硝化作用的影响。结果表明,森林土壤反硝化活性大于农田土壤,但农田土壤中Ｎ２Ｏ还原活性大于森林土壤,表现在农田和森林土壤中Ｎ２Ｏ／Ｎ２的产生比率分别为０．１１和３．６５。硝酸根和铵离子能促进两种土壤中的Ｎ２Ｏ产生,但可降低农田土壤中的Ｎ２Ｏ还原速率,与农田土壤相比,硝酸根可降低森林土壤Ｎ２     

Plant available phosphorus in homegarden and native forest soils under high rainfall in an equatorial humid tropics

Though the affinity of iron oxides and hydroxides for phosphorus (P) is thought to limit growth and productivity of plants on iron-rich acidic soils in humid tropical climate, tall trees are found in tropical rainforests, and vigorous growth occurs in herbaceous vegetation in the humid tropical climate of the Andamans. Our study reports how high rainfall influences Bray and Kurtz P-1 extractable P, water filled pore space (WFPS), microbial biomass carbon (MB-C) and phosphorus (MB-P) in the gravelly-sandy-loamy soils in three major land use systems: moist-evergreen forest, semi-evergreen forest and homegarden, in the equatorial humid tropical climate of South Andaman island of India. In addition, an ex-situ experiment investigated how labile carbon (glucose) under different soil-water regimes [25% field capacity (FC) and 100% FC] affected the P in the soils under the land use systems. WFPS, across the land use systems, was more than two times higher during the high rainfall than dry spell (72–80 hr after the high rainfall). The extractable P, across the land use systems, increased about 5 to 6 fold during the high rainfall than dry spell. The increase was the highest in the homegarden and lowest in moist-evergreen forest. The extractable P was positively correlated with the WFPS. MB-C and MB-P were lower during the high rainfall than dry spell in all the land use systems. In the ex-situ experiment, the extractable P increased 1.4 to 1.7 fold more in water (100% FC) + glucose than water (100% FC) alone treatment. Water at 25% FC did not increase the extractable P in the soils under all the land use systems. After cessation of the high rainfall, WFPS declined quickly within 2-hr in the upper layer (0–5 cm) of the soils. These indicate that the high rainfall together with labile carbon increases the extractable P through anaerobiosis, whereas, quick decline in the WFPS (0–5 cm) following cessation of the high rainfall helps its uptake by plants and microflora.     

Estimating base cation weathering rates in Canadian forest soils using a simple texture-based model

Mineral weathering is the primary source of long-term buffering capacity in soils and is important for forest nutrient sustainability. Regional assessments of weathering rates in Canada and the U.S. have employed an empirical clay-based Soil Texture Approximation (STA) owing to limited data availability, although the STA is rarely calibrated before application to a study area. Soil weathering rates estimated with the STA at 75 sites in Canadian forests (6–367 eq ha^?1 year^?1) were on average seven times lower than estimates obtained using the PROFILE model and when mineralogy was not available, the Analysis to Mineralogy model and parameter estimation (143–2,119 eq ha^?1 year^?1). Comparison with a catchment mass balance at a subset of sites in Ontario (n = 19) demonstrated the reliability of PROFILE weathering estimates. A revised (generalized) STA model for total base cation weathering was developed at the 75 study sites to incorporate soil silt content (%) and loss-on-ignition (LOI, %) (BC _w = (1.73 + 0.03 · silt ? 0.06 · LOI) · 1,000 · depth). The model performance (R _adj ²  = 73%) and relative bias (?1%) suggested that the revised STA may have broad application to forest soils in Canada but may not necessarily be suited to all soil texture classes.     

Enhanced iron availability by protein glycation may explain higher infection rates in diabetics

Serum proteins exist in a state of higher glycation among individuals with poor glycemic control, notably diabetics. These non-enzymatic modifications via the Maillard reaction have far reaching effects on metabolism and regulation, and may be responsible for increased infection rates within this population. Here we explore the effects of glycation on iron metabolism and innate immunity by investigating the interaction between siderophores and bovine serum albumin (BSA). Using a quartz crystal microbalance with dissipation monitoring to quantify association rates, glycated BSA exhibited a significantly reduced affinity for apo and holo enterobactin compared to a non-glycated BSA standard. Bacterial growth assays in the presence of BSA and under iron-limited conditions indicated the growth rate of enterobactin-producing E. coli increased significantly when the BSA was in a glycated form. The results, in addition to data in the literature, support the hypothesis that glycation of serum proteins may effectively increase the available free iron pool for bacteria in blood serum and weaken our innate immunity. This phenomenon may be partially responsible for higher infection rates in some diabetics, especially those with poor glycemic control.     

Presence of Nitrosospira cluster 2 bacteria corresponds to N transformation rates in nine acid Scots pine forest soils

The relation between environmental factors and the presence of ammonia-oxidising bacteria (AOB), and its consequences for the N transformation rates were investigated in nine Scots pine (Pinus sylvestris L.) forest soils. In general, the diversity in AOB appears to be strikingly low compared to other ecosystems. Nitrosospira cluster 2, as determined by temporal temperature gradient electrophoresis and sequencing, was the only sequence cluster detected in the five soils with high nitrification rates. In the four soils with low nitrification rates, AOB-like sequences could not be detected. Differences in nitrification rates between the forest soils correlated to soil C/N ratio (or total N) and atmospheric N deposition.     

Terrestrial wildlife responses to logging and fire in a Bolivian tropical humid forest

Logging and wildfire are significant anthropogenic disturbance agents in tropical forests. We compared the abundance and species richness of selected terrestrial wildlife taxa including small mammals, amphibians, reptiles, and terrestrial invertebrates in areas burned by wildfire and then logged and in adjacent undisturbed areas of a tropical humid forest in Bolivia. Disturbed areas had 24% less canopy cover than undisturbed areas but had 2.6 times the cover of large woody debris. Understory cover did not differ between disturbed and undisturbed areas. Small mammal abundance and species richness in disturbed areas were 43 and 70% higher, respectively, than in adjacent undisturbed areas. Herpetofaunal abundance did not differ significantly among disturbed and undisturbed areas, but trends for higher abundance were observed for both reptiles and amphibians in disturbed areas. Herpetofaunal species richness was significantly higher in disturbed compared to undisturbed areas. Total terrestrial invertebrate abundance, as estimated by pitfall traps, was significantly higher in undisturbed compared to disturbed areas mostly due to higher abundances of Formicidae and Blattidae. However, two invertebrate groups, Orthoptera and Lepidoptera (larvae) were more abundant in disturbed areas. Wildlife conservation strategies for areas where logging or wildfire occur should take into account species- or guild-specific responses to these disturbance agents.     

Mercury mobilization by chemical and microbial iron oxide reduction in soils of French Guyana

Iron oxy(hydr)oxides (oxides) are important mercury sinks in tropical oxisols and the geochemistry of these two elements are thus closely entwined. We hypothesized that bacterial Fe-oxide reduction in anoxic conditions could be a significant mechanism for mobilizing associated Hg. Iron oxide and mercury solubilisation in presence of two chemical reducers (ascorbate and dithionite, dissolving amorphous and amorphous plus well crystallized Fe-oxides, respectively) was compared to their solubilisation in presence of autochthonous ferri-reducing bacteria. This work was carried out on two soil profiles from a small catchment basin in French Guyana, an oxisol (O) from a well drained slope and a water-saturated hydromorphic soil (H). The chemical reductions showed that in the oxisol 20 and 48% of total Hg (Hg_T) was associated to amorphous and well crystallized iron oxides, respectively. However, in the hydromorphic soil, no Hg seemed to be associated to amorphous iron oxides while the well crystallized fraction contained less than 9% of Hg_T. Chemical Fe-oxide reduction showed that Hg solubility was correlated to Fe reduction in the oxisol, demonstrating a relationship between the geochemistry of these two metals. During bacterial growth, while bacterial iron reduction solubilised up to 3.2 mg Fe g^?1 soil in the oxisol sample, Hg_T remained unchanged. No mercury was detected in the culture medium either. However, chemical analysis showed a decrease of the amounts of Hg associated to amorphous and well crystallized Fe-oxides after 14 days of incubation, underlining the potential for iron-reducing bacteria to modify mercury distribution in soil.     

Aurintricarboxylic acid structure modifications lead to reduction of inhibitory properties against virulence factor YopH and higher cytotoxicity

Yersinia sp. bacteria owe their viability and pathogenic virulence to the YopH factor, which is a highly active bacterial protein tyrosine phosphatase. Inhibition of YopH phosphatase results in the lack of Yersinia sp. pathogenicity. We have previously described that aurintricarboxylic acid inhibits the activity of YopH at nanomolar concentrations and represents a unique mechanism of YopH inactivation due to a redox process. This work is a continuation of our previous studies. Here we show that modifications of the structure of aurintricarboxylic acid reduce the ability to inactivate YopH and lead to higher cytotoxicity. In the present paper we examine the inhibitory properties of aurintricarboxylic acid analogues, such as eriochrome cyanine R (ECR) and pararosaniline. Computational docking studies we report here indicate that ATA analogues are not precluded to bind in the YopH active site and in all obtained binding conformations ECR and pararosaniline bind to YopH active site. The free binding energy calculations show that ECR has a stronger binding affinity to YopH than pararosaniline, which was confirmed by experimental YopH enzymatic activity studies. We found that ATA analogues can reversibly reduce the enzymatic activity of YopH, but possess weaker inhibitory properties than ATA. The ATA analogues induced inactivation of YopH is probably due to oxidative mechanism, as pretreatment with catalase prevents from inhibition. We also found that ATA analogues significantly decrease the viability of macrophage cells, especially pararosaniline, while ATA reveals only slight effect on cell viability.     

Dissimilatory iron reduction and potential methane production in Chagan Lake wetland soils with carbon addition

Wetlands Ecology and Management - Dissimilatory iron reduction is increasingly becoming recognized as an influential process in freshwater sediments, coupling with carbon cycling. To evaluate the...     

Changes in organic phosphorus composition in boreal forest humus soils: the role of iron and aluminium

Organic phosphorus (P) is an important component of boreal forest humus soils, and its concentration has been found to be closely related to the concentration of iron (Fe) and aluminium (Al). We used solution and solid state ³¹P NMR spectroscopy on humus soils to characterize organic P along two groundwater recharge and discharge gradients in Fennoscandian boreal forest, which are also P sorption gradients due to differences in aluminium (Al) and iron (Fe) concentration in the humus. The composition of organic P changed sharply along the gradients. Phosphate diesters and their degradation products, as well as polyphosphates, were proportionally more abundant in low Al and Fe sites, whereas phosphate monoesters such as myo-, scyllo- and unknown inositol phosphates dominated in high Al and Fe soils. The concentration of inositol phosphates, but not that of diesters, was positively related to Al and Fe concentration in the humus soil. Overall, in high Al and Fe sites the composition of organic P seemed to be closely associated with stabilization processes, whereas in low Al and Fe sites it more closely reflected inputs of organic P, given the dominance of diesters which are generally assumed to constitute the bulk of organic P inputs to the soil. These gradients encompass the broad variation in soil properties detected in the wider Fennoscandian boreal forest landscape, as such our findings provide insight into the factors controlling P biogeochemistry in the region but should be of relevance to boreal forests elsewhere.     

Near-critical fluctuations and cytoskeleton-assisted phase separation lead to subdiffusion in cell membranes

Mechanosensitive channels, inner membrane proteins of bacteria, open and close in response to mechanical stimuli such as changes in membrane tension during osmotic stress. In bacteria, these channels act as safety valves preventing cell lysis upon hypoosmotic cell swelling: the channels open under membrane tension to release osmolytes along with water. The mechanosensitive channel of small conductance, MscS, consists, in addition to the transmembrane channel, of a large cytoplasmic domain (CD) that features a balloon-like, water filled chamber opening to the cytoplasm through seven side pores and a small distal pore. The CD is apparently a molecular sieve covering the channel that optimizes loss of osmolytes during osmoadaptation. We employ diffusion theory and molecular dynamics simulations to explore the transport kinetics of Glu⁻ and K⁺ as representative osmolytes. We suggest that the CD indeed acts as a filter that actually balances passage of Glu⁻ and K⁺, and possibly other positive and negative osmolytes, to yield a largely neutral efflux and, thereby, reduce cell depolarization in the open state and conserve to a large degree the essential metabolite Glu⁻.     

Competition can lead to unexpected patterns in tropical ant communities

Ecological communities are structured by competitive, predatory, mutualistic and parasitic interactions combined with chance events. Separating deterministic from stochastic processes is possible, but finding statistical evidence for specific biological interactions is challenging. We attempt to solve this problem for ant communities nesting in epiphytic bird’s nest ferns (Asplenium nidus) in Borneo’s lowland rainforest. By recording the frequencies with which each and every single ant species occurred together, we were able to test statistically for patterns associated with interspecific competition. We found evidence for competition, but the resulting co-occurrence pattern was the opposite of what we expected. Rather than detecting species segregation—the classical hallmark of competition—we found species aggregation. Moreover, our approach of testing individual pairwise interactions mostly revealed spatially positive rather than negative associations. Significant negative interactions were only detected among large ants, and among species of the subfamily Ponerinae. Remarkably, the results from this study, and from a corroborating analysis of ant communities known to be structured by competition, suggest that competition within the ants leads to species aggregation rather than segregation. We believe this unexpected result is linked with the displacement of species following asymmetric competition. We conclude that analysing co-occurrence frequencies across complete species assemblages, separately for each species, and for each unique pairwise combination of species, represents a subtle yet powerful way of detecting structure and compartmentalisation in ecological communities.     

Contribution of amino compounds to dissolved organic nitrogen in forest soils

Dissolved organic nitrogen (DON) may play an important role in plantnutrition and nitrogen fluxes in forest ecosystems. In spite of the apparentimportance of DON, there is a paucity of information concerning its chemicalcomposition. However, it is exactly this chemical characterization that isrequired to understand the importance of DON in ecosystem processes. Theprimaryobjective of this study was to characterize the distribution of free aminoacidsand hydrolyzable peptides/proteins in the DON fraction of Oa horizon leachatesalong an extreme edaphic gradient in northern California. Insitu soil solutions were extracted by centrifugation from Oahorizonscollected beneath Pinus muricata (Bishop pine) andCupressus pygmaea (pygmy cypress) on slightlyacidic/fertile and highly acidic/infertile sites. DON accounted for 77 to99% of the total dissolved nitrogen in Oa horizon leachates. Nitrogen infree amino acids and alkyl amines ranged from 0.04–0.07 mgN/L on the low fertility site to 0.45–0.49 mg N/L onthe high fertility site, and accounted for 1.5 to 10.6% of the DON fraction.Serine, glutamic acid, leucine, ornithine, alanine, aspartic acid andmethylamine were generally the most abundant free amino compounds. Combinedamino acids released by acid hydrolysis accounted for 48 to 74% of theDON, suggesting that proteins and peptides were the main contributor to DON inOa horizon leachates. Together, nitrogen from free andcombined amino compounds accounted for 59 to 78% of the DON. Most of theDON was found in the hydrophobic fraction, which suggests the presence ofprotein/peptide-polyphenol complexes or amino compounds associated withhumic substances. Because free and combined amino acids can be an importantnitrogen source for some plants, soil DON may play an important role in plantnutrition and ecosystem function.