Deforestation alters denitrification in a lowland tropical rain forest

Denitrification and the challenge of scaling microsite knowledge to the globe

Our knowledge of microbial processes-who is responsible for what, the rates at which they occur, and the substrates consumed and products produced-is imperfect for many if not most taxa, but even less is known about how microsite processes scale to the ecosystem and thence the globe. In both natural and managed environments, scaling links fundamental knowledge to application and also allows for global assessments of the importance of microbial processes. But rarely is scaling straightforward: More often than not, process rates in situ are distributed in a highly skewed fashion, under the influence of multiple interacting controls, and thus often difficult to sample, quantify, and predict. To date, quantitative models of many important processes fail to capture daily, seasonal, and annual fluxes with the precision needed to effect meaningful management outcomes. Nitrogen cycle processes are a case in point, and denitrification is a prime example. Statistical models based on machine learning can improve predictability and identify the best environmental predictors but are-by themselves-insufficient for revealing process-level knowledge gaps or predicting outcomes under novel environmental conditions. Hybrid models that incorporate well-calibrated process models as predictors for machine learning algorithms can provide both improved understanding and more reliable forecasts under environmental conditions not yet experienced. Incorporating trait-based models into such efforts promises to improve predictions and understanding still further, but much more development is needed.

Carbon Footprint Management by Agricultural Practices

Global attention to climate change issues, especially air temperature changes, has drastically increased over the last half-century. Along with population growth, greater surface temperature, and higher greenhouse gas (GHG) emissions, there are growing concerns for ecosystem sustainability and other human existence on earth. The contribution of agriculture to GHG emissions indicates a level of 18% of total GHGs, mainly from carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O). Thus, minimizing the effects of climate change by reducing GHG emissions is crucial and can be accomplished by truly understanding the carbon footprint (CF) phenomenon. Therefore, the purposes of this study were to improve understanding of CF alteration due to agricultural management and fertility practices. CF is a popular concept in agro-environmental sciences due to its role in the environmental impact assessments related to alternative solutions and global climate change. Soil moisture content, soil temperature, porosity, and water-filled pore space are some of the soil properties directly related to GHG emissions. These properties raise the role of soil structure and soil health in the CF approach. These properties and GHG emissions are also affected by different land-use changes, soil types, and agricultural management practices. Soil management practices globally have the potential to alter atmospheric GHG emissions. Therefore, the relations between photosynthesis and GHG emissions as impacted by agricultural management practices, especially focusing on soil and related systems, must be considered. We conclude that environmental factors, land use, and agricultural practices should be considered in the management of CF when maximizing crop productivity.

Short-Term Litter Manipulations have Strong Impact on Soil Nitrogen Dynamics in Larix gmelinii Forest of Northeast China

Changes in above-ground litterfall can influence below-ground biogeochemical processes in forests, which substantially impacts soil nitrogen (N) and nutrient cycling. However, how these soil processes respond to the litter manipulation is complex and poorly understood, especially in the N-limiting boreal forest. We aimed to examine how soil N dynamics respond to litter manipulations in a boreal larch forest. A litter manipulation experiment including control, litter exclusion, and litter addition was performed in the Larix gmelinii forest on the north of the Daxing’an Mountains in China. Monthly soil inorganic N, microbial biomass and the rate of net N mineralization in both 0–10 cm and 10–20 cm layers, and N2O flux were analyzed from May 2018 to October 2018. In 0–20 cm soil layer the average soil inorganic N contents, microbial biomass N (MBN) contents, the rate of net N mineralization (Rmin), and the soil N2O emission in the litter addition plot were approximately 40.58%, 54.16%, 128.57%, and 38.52% greater, respectively than those in the control. While litter exclusion reduced those indexes about 29.04%, 19.84%, 80.98%, and 31.45%, respectively. Compared with the dynamics of the 10–20 cm soil layer, the N dynamics in 0–10 cm soil were more sensitive to litter manipulation. Rmin and N2O emissions were significantly correlated with MBN in most cases. Our results highlight the short-term effects of litter manipulations on soil N dynamics, which suggests that the influence of litter on soil N process should be considered in the future defoliation management of the boreal larch forest.

Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils

Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.

Greenhouse gas emissions from sub-tropical agricultural soils after addition of organic by-products

As the cost of mineral fertilisers increases globally, organic soil amendments (OAs) from agricultural sources are increasingly being used as substitutes for nitrogen. However, the impact of OAs on the production of greenhouse gases (CO₂ and N₂O) is not well understood. A 60-day laboratory incubation experiment was conducted to investigate the impacts of applying OAs (equivalent to 296 kg N ha^-1 on average) on N₂O and CO₂ emissions and soil properties of clay and sandy loam soils from sugar cane production. The experiment included 6 treatments, one being an un-amended (UN) control with addition of five OAs being raw mill mud (MM), composted mill mud (CM), high N compost (HC), rice husk biochar (RB), and raw mill mud plus rice husk biochar (MB). These OAs were incubated at 60, 75 and 90% water-filled pore space (WFPS) at 25°C with urea (equivalent to 200 kg N ha^-1) added to the soils thirty days after the incubation commenced. Results showed WFPS did not influence CO₂ emissions over the 60 days but the magnitude of emissions as a proportion of C applied was RB < CM < MB < HC < MM. Nitrous oxide emissions were significantly less in the clay soil compared to the sandy loam at all WFPS, and could be ranked RB < MB < MM < CM < UN < HC. These results led to linear models being developed to predict CO₂ and N₂O emissions as a function of the dry matter and C/N ratio of the OAs, WFPS, and the soil CEC. Application of RB reduced N₂O emissions by as much as 42-64% depending on WFPS. The reductions in both CO₂ and N₂O emissions after application of RB were due to a reduced bioavailability of C and not immobilisation of N. These findings show that the effect of OAs on soil GHG emissions can vary substantially depending on their chemical properties. OAs with a high availability of labile C and N can lead to elevated emissions of CO₂ and N₂O, while rice husk biochar showed potential in reducing overall soil GHG emissions.

Relationships among net primary productivity, nutrients and climate in tropical rain forest: a pan-tropical analysis

Tropical rain forests play a dominant role in global biosphere-atmosphere CO(2) exchange. Although climate and nutrient availability regulate net primary production (NPP) and decomposition in all terrestrial ecosystems, the nature and extent of such controls in tropical forests remain poorly resolved. We conducted a meta-analysis of carbon-nutrient-climate relationships in 113 sites across the tropical forest biome. Our analyses showed that mean annual temperature was the strongest predictor of aboveground NPP (ANPP) across all tropical forests, but this relationship was driven by distinct temperature differences between upland and lowland forests. Within lowland forests (< 1000 m), a regression tree analysis revealed that foliar and soil-based measurements of phosphorus (P) were the only variables that explained a significant proportion of the variation in ANPP, although the relationships were weak. However, foliar P, foliar nitrogen (N), litter decomposition rate (k), soil N and soil respiration were all directly related with total surface (0-10 cm) soil P concentrations. Our analysis provides some evidence that P availability regulates NPP and other ecosystem processes in lowland tropical forests, but more importantly, underscores the need for a series of large-scale nutrient manipulations - especially in lowland forests - to elucidate the most important nutrient interactions and controls.

Late glacial stage and holocene tropical ice core records from huascaran, peru

Two ice cores from the col of Huascarán in the north-central Andes of Peru contain a paleoclimatic history extending well into the Wisconsinan (Würm) Glacial Stage and include evidence of the Younger Dryas cool phase. Glacial stage conditions at high elevations in the tropics appear to have been as much as 8 degrees to 12 degrees C cooler than today, the atmosphere contained about 200 times as much dust, and the Amazon Basin forest cover may have been much less extensive. Differences in both the oxygen isotope ratio zeta(18)O (8 per mil) and the deuterium excess (4.5 per mil) from the Late Glacial Stage to the Holocene are comparable with polar ice core records. These data imply that the tropical Atlantic was possibly 5 degrees to 6 degrees C cooler during the Late Glacial Stage, that the climate was warmest from 8400 to 5200 years before present, and that it cooled gradually, culminating with the Little Ice Age (200 to 500 years before present). A strong warming has dominated the last two centuries.

Biomass burning in the tropics: impact on atmospheric chemistry and biogeochemical cycles

Biomass burning is widespread, especially in the tropics. It serves to clear land for shifting cultivation, to convert forests to agricultural and pastoral lands, and to remove dry vegetation in order to promote agricultural productivity and the growth of higher yield grasses. Furthermore, much agricultural waste and fuel wood is being combusted, particularly in developing countries. Biomass containing 2 to 5 petagrams of carbon is burned annually (1 petagram = 10(15) grams), producing large amounts of trace gases and aerosol particles that play important roles in atmospheric chemistry and climate. Emissions of carbon monoxide and methane by biomass burning affect the oxidation efficiency of the atmosphere by reacting with hydroxyl radicals, and emissions of nitric oxide and hydrocarbons lead to high ozone concentrations in the tropics during the dry season. Large quantities of smoke particles are produced as well, and these can serve as cloud condensation nuclei. These particles may thus substantially influence cloud microphysical and optical properties, an effect that could have repercussions for the radiation budget and the hydrological cycle in the tropics. Widespread burning may also disturb biogeochemical cycles, especially that of nitrogen. About 50 percent of the nitrogen in the biomass fuel can be released as molecular nitrogen. This pyrdenitrification process causes a sizable loss of fixed nitrogen in tropical ecosystems, in the range of 10 to 20 teragrams per year (1 teragram = 10(12) grams).

Export of nitrogenous compounds due to incomplete cycling within biological soil crusts of arid lands

Second only to water among limiting factors, nitrogen controls the fertility of most arid regions. Where dry and wet depositions are weak, as in the western US deserts, N inputs rely heavily on biological N(2) fixation. Topsoil cyanobacterial communities known as biological soil crusts (BSCs) are major N(2) fixation hot spots in arid lands, but the fate of their fixed N remains controversial. Using a combination of microscale and mesoscale process rate determinations, we found that, in spite of theoretically optimal conditions, denitrification rates in BSCs were paradoxically immaterial for nitrogen cycling. Denitrifier populations within BSCs were extremely low. Because of this absence of denitrification, and because of the limitation of respiration and ammonia oxidation by diffusive O(2) supply, we could demonstrate that BSCs function as net exporters of ammonium, nitrate and organic N to the soils they cover, in approximately stoichiometrically equal proportions. Overall export rates during periods of biological activity are in the range of tens to hundreds of mumol-N m(-2) h(-1), commensurate with those of N(2) fixation. These results explain the long-term dependence of BSCs on N(2) fixation, confirm their role in landscape fertility, and provide a robust argument for conservation of these endangered communities.

Influence of soil moisture and land use history on denitrification end-products

We investigated the effects of recent moisture history on the relative production of N2O and N2 during denitrification in soil from cropped and successional ecosystems. The soils were pedogenically identical but had been managed differently for the past decade. Sieved soils were amended with nitrate, glucose, and water. Long-wet and short-wet incubations received 80 and 0%, respectively, of prescribed water 2 d before incubation and the rest just before incubation. The N2O and N2 production and N2O mole fraction (N2O/[N2O + N2]) were measured using acetylene inhibition. The N2 production and soil 15N enrichment were measured by 15N-gas evolution. The response of N2O mole fraction to moisture history differed by ecosystem. Mean N2O mole fraction in the successional system was about the same for long-wet and short-wet treatments (0.34 and 0.33, respectively). For the cropped system, however, the N2O mole fraction was 0.36 for the long-wet and 0.90 for the short-wet treatment. Thus, in the cropped system a much smaller proportion of end product was N2O if soil had been wet for 2 d. For N2 fluxes, the isotope method gave the same pattern (r = 0.92) but only about one-third the magnitude, suggesting that N2 derived from two distinct pools. Differences in response of N2O mole fraction for successional and cropped soils may be due to differences in microbial communities. Further knowledge of ecosystem differences with respect to N2O mole fraction and recent moisture history may improve modeled estimates of local and global N2O fluxes.

Sequence signals in eukaryotic upstream regions

Two DNA sequence elements are known to recur frequently upstream of eukaryotic polymerase II-transcribed genes. The TATAAA, at position -40, specifies the transcription initiation site. The GGCCAATCT is less frequent around -80. Sequence analysis of upstream regions reveals that the underlined yeast UAS2 consensus sequence, TGATTGGT, is also very frequent at -80 in higher polymerase II-transcribed animal sequences. The underlined CCAAT box and yeast UAS sequences are complementary. Structural analysis suggests some symmetry in their DNA structures. Upstream of the TATAAT-rich region there is an abundance of GC sequences. Analysis of nucleotide tracts indicates that these are preferentially flanked by their complementary nucleotides with a pyrimidine-purine junction, i.e., TTAN, CCGn, CnGG, TnAA. Here, I discuss DNA structural consideration in upstream regions along with protein readout of the major and minor groove information content. These sequence-structure aspects are put in the general context of protein (factors)-DNA (elements) recognition and regulation.

The nucleoskeleton and the topology of transcription

Transcription is conventionally believed to occur by passage of a mobile polymerase along a fixed template. Evidence for this model is derived almost entirely from material prepared using hypotonic salt concentrations. Studies on subnuclear structures isolated using hypertonic conditions, and more recently using conditions closer to the physiological, suggest an alternative. Transcription occurs as the template moves past a polymerase attached to a nucleoskeleton; this skeleton is the active site of transcription. Evidence for the two models is summarised. Much of it is consistent with the polymerase being attached and not freely diffusible. Some consequences of such a model are discussed.

The domain model for eukaryotic DNA organization. 2: A molecular basis for constraints on development and evolution

A model for eukaryotic DNA organization has been proposed in which DNA regulatory processes depend on multiple site-specific DNA-nuclear matrix interactions throughout a DNA domain. In this model gene regulation depends on combinations of a few control factors in a cell to activate cell type-specific genes. This model suggests simple molecular mechanisms for organismal development which can account for sequential activation of appropriate groups of genes throughout development and for specific constraints on developmental pathways. Additionally, these suggested developmental pathways are consistent with mechanisms of evolution in which gradualism and punctuated equilibrium are not exclusive of one another and are interrelated mechanisms of evolution that are both induced by specific chromosomal mutations.

DNA sequences regulating human globin gene transcription in nondeletional hereditary persistence of fetal hemoglobin

Strong genetic evidence supports the idea that point mutations in the promoter of gamma-globin genes overexpressed in adult age [hereditary persistence of fetal hemoglobin (HPFH)] are responsible for the observed phenotype. DNA binding sites for ubiquitous and/or erythroid specific nuclear proteins correlate in location with the positions of point mutations responsible for HPFH. The analysis of the effects of one of these mutations (-175 T greater than C) on in vitro binding of nuclear proteins and on the activity of the mutated promoter in transfection assays indicates that altered binding of the erythroid-specific protein NFE-1 may be responsible for increased activity of the mutated promoter. Other HPFH mutations close to the distal CCAAT box (-117 G greater than A and 13 nucleotide deletions, -114 to -102) have complex effects on in vitro binding of nuclear proteins; their only common effect is the loss of binding of the erythroid-specific factor NFE3. If mechanisms generating the HPFH phenotype are homogeneous, NFE3 might be a negatively acting factor; alternatively, heterogeneous mechanisms might operate and HPFH might additionally be related to loss of binding to the distal CCAAT box region of either NFE1 (-117 HPFH) or of the ubiquitous CCAAT displacement protein-CDP (13 nucleotides deletion). Finally, it is also proposed that increased activity of the HPFH promoters may secondarily cause decreased expression of the delta- and beta-globin genes in cis possibly by competition between gamma- and beta-globin promoters for interaction with common regulatory elements.